Nucleic acid detection assay control genes

ABSTRACT

The present invention includes methods of normalizing quantitative and non-quantitative nucleic acid detection as-says by monitoring control genes. These methods have applicability across a broad spectrum of hybridization format.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application60/305,154 (filed Jul. 16, 2001), which is herein incorporated byreference in its entirety.

FIELD OF THE INVENTION

The invention relates generally to control genes that may be utilizedfor normalizing hybridization and/or amplification reactions.

BACKGROUND OF THE INVENTION

Nucleic acid hybridization and other quantitative nucleic acid detectionassays are routinely used in medical and biotechnological research anddevelopment, diagnostic testing, drug development and forensics. Suchtechnologies have been used to identify genes which are up- ordown-regulated in various disease or physiological states, to analyzethe roles of the members of cellular signaling cascades and to identifydruggable targets for various disease and pathology states.

Examples of technologies commonly used for the detection and/orquantification of nucleic acids include northern blotting (Krumlauf(1994) Mol Biotechnol 2(3), 227-242), ill situ hybridization (Parker &Barnes (1999) Methods Mol Biol. 106, 247-83), RNAse protection assays(Hod (1992) Biotechniques 13(6), 852-854; Saccomanno et al. (1992)Biotechniques 13(6):846-50), microarrays, and reverse transcriptionpolymerase chain reaction (RT-PCR) (see Bustin, (2000) Journal ofMolecular Endocrinology 25, 169-193).

The reliability of these nucleic acid detection methods depend on theavailability of accurate means for accounting for variations betweenanalyses. For example, variations in hybridization conditions, labelintensity, reading and detector efficiency, sample concentration andquality, background effects, and image processing effects eachcontribute to signal heterogeneity. Hegde et al. (2000) Biotechniques29(3): 548-562; Berger et al. (2000) WO 00/04188. Normalizationprocedures used to overcome these variations often rely on controlhybridizations to housekeeping genes such as β-actin,glyceraldehyde-3-phosphate dehydrogenase, and the transferrin receptorgene. Eickhoffet al. (1999) Nucleic Acids Research 27(22): e33; Spiesset al. (1999) Biotechniques 26(1): 46-50. These methods, however,generally do not provide the signal linearity sufficient to detect smallbut significant changes in transcription or gene expression. Spiess etal. (1999) Biotechniques 26(1): 46-50. In addition, the steady statelevels of many housekeeping genes are susceptible to alterations inexpression levels that are dependent on cell differentiation,nutritional state, specific experimental and stimulation protocols.Eickhoffet al. (1999) Nucleic Acids Research 27(22): e33; Spiess et al.(1999) Biotechniques 26(1): 46-50; Hegde et al. (2000)Biotechniques29(3): 548-562; and Berger et al. (2000) WO 00/04188. Consequently,there exists a need for the identification and use of additional genesthat may serve as effective controls in nucleic acid detection assays.

SUMMARY OF THE INVENTION

The present invention includes methods of identifying at least one genethat is consistently expressed across different cell or tissue types inan organism, comprising: preparing gene expression profiles fordifferent cell or tissue types from the organism; calculating acoefficient of variation for at least one gene in each of the profilesacross the different cell or tissue types; and selecting any gene whosecoefficient of variation indicates that the gene is consistentlyexpressed across the different cell or tissue types. The coefficient ofvariation may be less than about 40% and the methods may comprisecreating gene expression profiles for about 10, 25, 50, 100 or moredifferent cell or tissue types. The gene expression profiles may beprepared be querying a gene expression database.

The invention also includes a set of probes comprising at least twoprobes that specifically hybridize to a control gene identified by themethods of the invention. Such sets of probes may comprise probes thatspecifically hybridize to at least about 10, 25, 50 or 100 controlgenes. In some formats, the sets of probes are attached to a solidsubstrate such as a microarray or chip.

The invention also includes methods of normalizing the data from anucleic acid detection assay comprising: detecting the expression levelfor at least one gene in a nucleic acid sample; and normalizing theexpression of said at least one gene with the detected expression of atleast one control gene identified by the method of the invention. Thenumber of control genes used to normalize gene expression data maycomprise about 10, 25, 50, 100 or more of the control genes hereinidentified.

In another embodiment, the invention includes a set of probes comprisingat least two probes that specifically hybridize to a gene of Table 1 orTable 2. The set may comprise at least about 10, 25, 50, 100 or more thecontrol genes of Table 1 or Table 2. The sets of probes may or may notbe attached to a solid substrate such as a chip.

The invention, in another embodiment, includes methods of normalizingthe data from a nucleic acid detection assay comprising: detecting theexpression level for at least one gene in a nucleic acid sample; andnormalizing the expression of said at least one gene with the detectedexpression of at least one control gene of Table 1 or Table 2. Thenumber of control genes used to normalize gene expression data maycomprise about 10, 25, 50, 100 or more of the control genes hereinidentified.

DETAILED DESCRIPTION

The present Inventors have identified control genes that may bemonitored in nucleic acid detection assays and whose expression levelsmay be used to normalize gene expression data. Normalization of geneexpression data from a cell or tissue sample with the expressionlevel(s) of the identified genes allows the accurate assessment of theexpression level(s) for genes that are differentially regulated betweensamples, tissues, treatment conditions, etc. These genes may be usedacross a broad spectrum of assay formats, but are particularly useful inmicroarray or hybridization based assay formats.

A. Nucleic Acid Detection Assay Controls

1. Selection of Control Genes

As used herein, the genes and nucleic acids of Tables 1 and 2 arereferred to as “control genes.”

Control genes of the invention are produced by a method comprisingpreparing gene expression profiles (a representation of the expressionlevel for at least one gene, preferably 10, 50, 100 or more, or mostpreferably nearly all or all expressed genes in a sample) from a varietyof cell or tissue types, measuring the level of expression for at leastone gene in each of the gene expression profiles to produce geneexpression data, calculating a coefficient of variation from the geneexpression data for each gene and selecting genes whose coefficient ofvariation indicates that the gene is consistently expressed at about thesame level in the different cell or tissue types.

The gene expression profile may be produced by any means of quantifyinggene expression for at least one gene in the tissue or cell sample. Inpreferred methods, gene expression is quantified by a method selectedfrom the group consisting of a hybridization assay or an amplificationassay. Hybridization assays may be any assay format, such as thisdescribed below, that relies on the hybridization of a probe or primerto a nucleic acid molecule in the sample. Such formats include, but arenot limited to, differential display formats and microarrayhybridization, including microarrays produced in chip format.Amplification assays include, but are not limited to, quantitative PCR,semiquantitative PCR and assays that rely on amplification of nucleicacids subsequent to the hybridization of the nucleic acid to a probe orprimer. Such assays include the amplification of nucleic acid moleculesfrom a sample that are bound to a microarray or chip.

In other circumstances, gene expression profiles may be produced byquerying a gene expression database comprising expression results forgenes from various cell or tissue samples. The gene expression resultsin the database may be produced by any available method, such asdifferential display methods and microarray-based hybridization methods.The gene expression profile is typically produced by the step ofquerying the database with the identity of a specific cell or tissuetype for the genes that are expressed in the cell or tissue type and/orthe genes that are differentially regulated compared to a control cellor tissue sample. Available databases include, but are not limited to,the Gene Logic GeneExpress® database, the Gene Expression Omnibus geneexpression and hybridization array repository available through NCBI(www.ncbi.nln.nih.gov/entrez) and the SAGE™ gene expression database.

The cell or tissue samples that are used to prepare gene expressionprofiles may include any cell or tissue sample available. Such samplesinclude, but are not limited to, tissues removed as surgical samples,diseased or normal tissues, in vitro or in vivo grown cells, cellculture and cells or tissues exposed to an agent such as a toxin. Thenumber of samples required to calculate a coefficient of variation isvariable, but may include about 10, 25, 50, 100, 200, 500 or more cellor tissue samples. The cell or tissue samples may be derived from ananimal or plant, preferably a mammal. In some instances, the cell ortissue samples may be human, canine (dog), mouse or rat in origin.

The coefficient of variation may be calculated from raw expression dataor from data that has been normalized to control for the mechanics ofhybridization, such as data normalized or controlled for backgroundnoise due to non-specific hybridization. Such data typically includes,but is not limited to, fluorescence readings from microarray basedhybridizations, densitometry readings produced from assays that rely onradiological labels to detect and quantify gene expression and dataproduced from quantitative or semi-quantitative amplification assays.

The coefficient of variation (% CV) is typically calculated bycalculating a mean value for the expression level of a given gene acrossa number of samples and calculating the standard deviation (SD) fromthat mean. The % CV may be calculated by the following equation: %CV=SD/Mean×100. Genes with a % CV of less than about 50% and preferablyless than about 40%, may be selected as control genes or are consideredas genes that are consistently expressed across the different cell ortissue types tested.

As used herein, “background” refers to signals associated withnon-specific binding (cross-hybridization). In addition tocross-hybridization, background may also be produced by intrinsicfluorescence of the hybridization format components themselves.

“Bind(s) substantially” refers to complementary hybridization between anoligonucleotide probe and a nucleic acid sample and embraces minormismatches that can be accommodated by reducing the stringency of thehybridization media to achieve the desired detection of the nucleic acidsample.

The phrase “hybridizing specifically to” refers to the binding,duplexing or hybridizing of a molecule substantially to or only to aparticular nucleotide sequence or sequences under stringent conditionswhen that sequence is present in a complex mixture (e.g., totalcellular) DNA or RNA.

2. Preparation of Controls Genes, Probes and Primers

The control genes listed in Tables 1 and 2 may be obtained from avariety of natural sources such as organisms, organs, tissues and cells.The sequences of known genes are in the public databases. The GenBankAccession Number corresponding to the Normalization Control Genes can befound in the third column of the Tables under “Exemplar Seq: Accession.”The sequences of the genes in GenBank (http://www.ncbi.nlin.nih.gov/)are herein incorporated by reference in their entirety.

Probes or primers for the nucleic acid detection assays described hereinthat specifically hybridize to a control gene may be produced by anyavailable means. For instance, probe sequences may be prepared bycleaving DNA molecules produced by standard procedures with commerciallyavailable restriction endonucleases or other cleaving agent. Followingisolation and purification, these resultant normalization control genefragments can be used directly, amplified by PCR methods or amplified byreplication or expression from a vector.

Control genes and control gene probes or primers (i.e., synthetic oligo-and polynucleotides) are most easily synthesized by chemical techniques,for example, the phosphotriester method of Matteucci, et al. ((1981) J.Am. Chem. Soc. 103: 3185-3191) or using automated synthesis methodsusing the GenBank sequences disclosed in Tables 1 and 2. In addition,larger nucleic acids can readily be prepared by well known methods, suchas synthesis of a group of oligonucleotides that define various modularsegments of the normalization control genes and normalization controlgene segments, followed by ligation of oligonucleotides to build thecomplete nucleic acid molecule.

B. Normalization Methods

Gene expression data produced from the control genes in a given sampleor samples may be used to normalize the gene expression data from othergenes using any available arithmatic or calculative means. Such methodsinclude, but are not limited, methods of data analysis described byHegde et al. (2000)Biotechiniques 29(3): 548-562; Winzeller et al.(1999) Meth. Enzymol. 306(1): 3-18; Tkatchenko et al. (2000) Biochimicaet Biophysica Acta 1500: 17-30; Berger et al. (2000) WO 00/04188;Schuchhardt et al. (2000) Nucleic Acids Research 28(10): e47; Eickhoffetal. (1999) Nucleic Acids Research 27(22): e33. Micro-array data analysisand image processing software packages and protocols, includingnormalization methods, are also available from BioDiscovery(http://www.biodiscovery.com/), Silicon Graphics(http://www.sigenetics.com), Spotfire (http://www.spotfire.com/),Stanford University (http://rana.Stanford.EDU/software/), National HumanGenome Research Institute(http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/img_analysis.html), TIGR(http://www.tigr.org/softlab/), and Affymetrix (affy and maffypaclkages), among others.

C. Assay or Hybridization Formats

The control genes of the present invention may be used in any nucleicacid detection assay format, including solution-based and solidsupport-based assay formats. As used herein, “hybridization assayformat(s)” refer to the organization of the oligonucleotide probesrelative to the nucleic acid sample. The hybridization assay formatsthat may be used with the control genes and methods of the presentinvention include assays where the nucleic acid sample is labeled withone or more detectable labels, assays where the probes are labeled withone or more detectable labels, and assays where the sample or the probesare immobilized. Hybridization assay formats include but are not limitedto: Northern blots, Southern blots, dot blots, solution-based assays,branched-DNA assays, PCR, RT-PCR, quantitative or semi-quantitativeRT-PCR, microarrays and biochips.

As used herein, “nucleic acid hybridization” simply involves contactinga probe and nucleic acid sample under conditions where the probe and itscomplementary target can form stable hybrid duplexes throughcomplementary base pairing (see Lockhart et al., (1999) WO 99/32660).The nucleic acids that do not form hybrid duplexes are then washed awayleaving the hybridized nucleic acids to be detected, typically throughdetection of an attached detectable label.

It is generally recognized that nucleic acids are denatured byincreasing the temperature or decreasing the salt concentration of thebuffer containing the nucleic acids.

Under low stringency conditions (e.g., low temperature and/or high salt)hybrid duplexes (e.g., DNA-DNA, RNA-RNA or RNA-DNA) will form even wherethe annealed sequences are not perfectly complementary. Thus,specificity of hybridization is reduced at lower stringency. Conversely,at higher stringency (e.g., higher temperature or lower salt) successfulhybridization requires fewer mismatches. One of skill in the art willappreciate that hybridization conditions may be selected to provide anydegree of stringency. In a preferred embodiment, hybridization isperformed at low stringency, in this case in 6×SSPE-T at 37° C. (0.005%Triton x-100) to ensure hybridization and then subsequent washes areperformed at higher stringency (e.g., 1×SSPE-T at 37° C.) to eliminatemismatched hybrid duplexes. Successive washes may be performed atincreasingly higher stringency (e.g., down to as low as 0.25×SSPET at37° C. to 50° C. until a desired level of hybridization specificity isobtained. Stringency can also be increased by addition of agents such asformamide. Hybridization specificity may be evaluated by comparison ofhybridization to the test probes with hybridization to the variouscontrols that can be present (e.g., expression level control,normalization control, mismatch controls, etc.).

As used herein, the term “stringent conditions” refers to conditionsunder which a probe will hybridize to a complementary control nucleicacid, but with only insubstantial hybridization to other sequences.Stringent conditions are sequence-dependent and will be different underdifferent circumstances. Longer sequences hybridize specifically athigher temperatures. Generally, stringent conditions are selected to beabout 5° C. lower than the thermal melting point (T_(m)) for thespecific sequence at a defined ionic strength and pH.

Typically, stringent conditions will be those in which the saltconcentration is at least about 0.01 to 1.0 M sodium ion concentration(or other salts) at pH 7.0 to 8.3 and the temperature is at least about30° C. for short probes (e.g., 10 to 50 nucleotide). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide.

In general, there is a tradeoff between hybridization specificity(stringency) and signal intensity. Thus, in a preferred embodiment, thewash is performed at the highest stringency that produces consistentresults and that provides a signal intensity greater than approximately10% of the background intensity. Thus, in a preferred embodiment, thehybridized array may be washed at successively higher stringencysolutions and read between each wash. Analysis of the data sets thusproduced will reveal a wash stringency above that the hybridizationpattern is not appreciably altered and which provides adequate signalfor the particular oligonucleotide probes of interest.

The “percentage of sequence identity” or “sequence identity” isdetermined by comparing two optimally aligned sequences or subsequencesover a comparison window or span, wherein the portion of thepolynucleotide sequence in the comparison window may optionally compriseadditions or deletions (i.e., gaps) as compared to the referencesequence (which does not comprise additions or deletions) for optimalalignment of the two sequences. The percentage is calculated bydetermining the number of positions at which the identical residue(e.g., nucleic acid base or amino-acid residue) occurs in both sequencesto yield the number of matched positions, dividing the number of matchedpositions by the total number of positions in the window of comparisonand multiplying the result by 100 to yield the percentage of sequenceidentity. Percentage sequence identity when calculated using theprograms GAP or BESTFIT (see below) is calculated using default gapweights. Sequences corresponding to the control genes of Tables 1 and 2may comprise at least about 70% sequence identity to the GenBank IDS ofthe genes in the Tables, preferably about 75%, 80% or 85% or morepreferably, about 90% or 95% or more identity.

Homology or identity is determined by BLAST (Basic Local AlignmentSearch Tool) analysis using the algorithm employed by the programsblastp, blastn, blastx, tblastn and tblastx (Karlin et al., (1990) Proc.Natl. Acad. Sci. USA 87, 2264-2268 and Altschul, (1993) J. Mol. Evol.36, 290-300, fully incorporated by reference) which are tailored forsequence similarity searching. The approach used by the BLAST program isto first consider similar segments between a query sequence and adatabase sequence, then to evaluate the statistical significance of allmatches that are identified and finally to summarize only those matcheswhich satisfy a preselected threshold of significance. For a discussionof basic issues in similarity searching of sequence databases, seeAltschul et al., (1994) Nature Genet. 6, 119-129) which is fullyincorporated by reference. The search parameters for histogram,descriptions, alignments, expect (i.e., the statistical significancethreshold for reporting matches against database sequences), cutoff,matrix and filter are at the default settings. The default scoringmatrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62matrix (Henilcoff et al., (1992) Proc. Natl. Acad. Sci. USA 89,10915-10919, fully incorporated by reference). Four blastn parameterswere adjusted as follows: Q=10 (gap creation penalty); R=10 (gapextension penalty); wink=1 (generates word hits at every wink^(th)position along the query); and gapw=16 (sets the window width withinwhich gapped alignments are generated). The equivalent Blastp parametersettings were Q=9; R=2; winkl; and gapw=32. A Bestfit comparison betweensequences, available in the GCG package version 10.0, uses DNAparameters GAP=50 (gap creation penalty) and LEN=3 (gap extensionpenalty) and the equivalent settings in protein comparisons are GAP=8and LEN=2.

As used herein a “probe” or “oligonucleotide probe” is defined as anucleic acid, capable of binding to a nucleic acid sample orcomplementary control gene nucleic acid through one or more types ofchemical bonds, usually through complementary base pairing, usuallythrough hydrogen bond formation. As used herein, a probe may includenatural (i.e., A, G, U, C or T) or modified bases (7-deazaguanosine,inosine, etc.). In addition, the bases in probes may be joined by alinkage other than a phosphodiester bond, so long as it does notinterfere with hybridization. Thus, probes may be peptide nucleic acidsin which the constituent bases are joined by peptide bonds rather thanphosphodiester linkages.

Probe arrays may contain at least two or more oligonucleotides that arecomplementary to or hybridize to one or more of the control genesdescribed herein. Such arrays may also contain oligonucleotides that arecomplementary or hybridize to at least about 2, 3, 5, 7, 10, 50, 100 ormore the genes described herein. Any solid surface to whicholigonucleotides or nucleic acid sample can be bound, either directly orindirectly, either covalently or non-covalently, can be used. Forexample, solid supports for various hybridization assay formats can befilters, polyvinyl chloride dishes, silicon or glass based chips, etc.Glass-based solid supports, for example, are widely available, as wellas associated hybridization protocols. (See, e.g., Beattie, WO95/11755).

A preferred solid support is a high density array or DNA chip. Thiscontains an oligonucleotide probe of a particular nucleotide sequence ata particular location on the array. Each particular location may containmore than one molecule of the probe, but each molecule within theparticular location has an identical sequence. Such particular locationsare termed features. There may be, for example, 2, 10, 100, 1000,10,000, 100,000, 400,000, 1,000,000 or more such features on a singlesolid support. The solid support, or more specifically, the area whereinthe probes are attached, may be on the order of a square centimeter.

1. Dot Blots

The control genes listed in Tables 1 and 2 and methods of the presentinvention may be utilized in numerous hybridization formats such as dotblots, dipstick, branched DNA sandwich and ELISA assays. Dot blothybridization assays provide a convenient and efficient method ofrapidly analyzing nucleic acid samples in a sensitive manner. Dot blotsare generally as sensitive as enzyme-linked immunoassays. Dot blothybridization analyses are well known in the art and detailed methods ofconducting and optimizing these assays are detailed in U.S. Pat. No.6,130,042 and 6,129,828, and Tkatchenlco et al. (2000) Biochimica etBiophysica Acta 1500: 17-30. Specifically, labeled or unlabeled nucleicacid sample is denatured and bound to a membrane (i.e. nitrocellulose),and is then contacted with unlabeled or labeled oligonucleotide probes.Buffer and temperature conditions can be adjusted to vary the degree ofidentity between the oligonucleotide probes and nucleic acid samplenecessary for hybridization.

Several modifications of the basic Dot blot hybridization format havebeen devised. For example, Reverse Dot blot analyses employ the samestrategy as the Dot blot method, except that the oligonucleotide probesare bound to the membrane and the nucleic acid sample is applied andhybridized to the bound probes. Similarly, the Dot blot hybridizationformat can be modified to include formats where either the nucleic acidsample or the oligonucleotide probe is applied to microtiter plates,microbeads or other solid substrates.

2. Membrane-Based Formats

Although each membrane-based format is essentially a variation of theDot blot hybridization format, several types of these formats arepreferred. Specifically, the methods of the present invention may beused in Northern and Southern blot hybridization assays. Although themethods of the present invention are generally used in quantitativenucleic acid hybridization assays, these methods may be used inqualitative or semi-quantitative assays such as Southern blots, in orderto facilitate comparison of blots. Southern blot hybridization, forexample, involves cleavage of either genomic or cDNA with restrictionendonucleases followed by separation of the resultant fragments on apolyacrylamide or agarose gel and transfer of the nucleic acid fragmentsto a membrane filter. Labeled oligonucleotide probes are then hybridizedto the membrane-bound nucleic acid fragments. In addition, intact cDNAmolecules may also be used, separated by electrophoresis, transferred toa membrane and analyzed by hybridization to labeled probes. Northernanalyses, similarly, are conducted on nucleic acids, either intact orfragmented, that are bound to a membrane. The nucleic acids in Northernanalyses, however, are generally RNA.

3. Arrays.

Any microarray platform or technology may be used to produce geneexpression data that may be normalized with the control genes andmethods of the invention. Oligonucleotide probe arrays can be made andused according to any techniques known in the art (see for example,Lockhart et al., (1996) Nat. Biotechnol. 14, 1675-1680; McGall et al.,(1996) Proc. Nat. Acad. Sci. USA 93, 13555-13460). Such probe arrays maycontain at least one or more oligonucleotides that are complementary toor hybridize to one or more of the nucleic acids of the nucleic acidsample and/or the control genes of Tables 1 and 2. Such arrays may alsocontain oligonucleotides that are complementary or hybridize to at least2, 3, 5, 7, 10, 50, 100 or more of the control genes listed in Tables 1and 2.

Control oligonucleotide probes of the invention are preferably ofsufficient length to specifically hybridize only to appropriate,complementary genes or transcripts. Typically the oligonucleotide probeswill be at least about 10, 12, 14, 16, 18, 20 or 25 nucleotides inlength. In some cases longer probes of at least 30, 40, or 50nucleotides will be desirable. The oligonucleotide probes of highdensity array chips include oligonucleotides that range from about 5 toabout 45 or 5 to about 500 nucleotides, more preferably from about 10 toabout 40 nucleotides and most preferably from about 15 to about 40nucleotides in length. In other particularly preferred embodiments theprobes are 20 or 25 nucleotides in length. In another preferredembodiment, probes are double or single strand DNA sequences. Theoligonucleotide probes are capable of specifically hybridizing to thecontrol gene nucleic acids in a sample.

One of skill in the art will appreciate that an enormous number of arraydesigns comprising control probes of the invention are suitable for thepractice of this invention. The high density array will typicallyinclude a number of probes that specifically hybridize to each controlgene nucleic acid, e.g. mRNA or cRNA. (See WO 99/32660 for methods ofproducing probes for a given gene or genes.) Assays and methodscomprising control probes of the invention may utilize available formatsto simultaneously screen at least about 100, preferably about 1000, morepreferably about 10,000 and most preferably about 500,000 or 1,000,000different nucleic acid hybridizations.

The methods and control genes of this invention may also be used tonormalize gene expression data produced using commercially availableoligonucleotide arrays that contain or are modified to contain controlgene probes or the invention. A preferred oligonucleotide array may beselected from the Affymetrix, Inc. GeneChip® series of arrays whichinclude the GeneChip® Human Genome U95 Set, GeneChip® Hu35K Set,GeneChip®, HuGeneFL Array, GeneChip® Human Cancer G110 Array, GeneChip®Rat Genome U34 Set, GeneChip® Mu19K Set, GeneChip® Mu11K Set, GeneChip®Yeast Genome S98 Array, GeneChip® E. coli Genome Array, GeneChip®Arabidopsis Genome Array, GeneChip® HuSNP™ Probe Array, GeneChip®GenFlex™ Tag Array, GeneChip® HIV PRT Plus Probe Array, GeneChip® P53Probe Array, GeneChip®, and the CYP450 Probe Array. In anotherembodiment, an oligonucleotide array may be selected from the IncytePharmaceuticals, Inc. GEM™ series of arrays which includes the UniGEM™ V2.0, Human Genome GEM 1, Human Genome GEM 2, Human Genome GEM 3, HumanGenome GEM 4, Human Genome GEM 5, LifeGEM™ 1 Cancer/Signal Peptide,LifeGEM 2 Inflammation/Blood, Mouse GEM 1 Rat GEM 1 Liver/Kidney,Rat GEM2 Central Nervous System, Rat GEM 3 Liver/Kidney, S. aureus GEM 1, C.albicans GEM 1, and Arabidopsis GEM.

4. RT-PCR

The control genes and methods of the invention may be used in any typeof polymerase chain reaction. A preferred PCR format is reversetransciptase polymerase chain reaction (RT-PCR), an in vitro method forenzymatically amplifying defined sequences of RNA (Rappolee et al.,(1988) Science 241, 708-712) permitting the analysis of differentsamples from as little as one cell in the same experiment (See Arubion:RT-PCR: The Basics; M. J. McPherson and S. G. Møller, PCR BIOSScientific Publishers Ltd Oxford, OX4 1RE (2000); Dieffenbach et al.,PCR Primer: A Laboratory Manual Cold Spring Harbor Laboratory Press 1995for review). One of ordinary skill in the art may appreciate theenormous number of variations in RT-PCR platforms that are suitable forthe practice of the invention, including complex variations aimed atincreasing sensitivity such as semi-nested (Wasserman et al., (1999)Molecular Diagnostics 4, 21-28), nested (Israeli et al., (1994) CancerResearch 54, 6303-6310; Soeth et al., (1996) International Journal ofCancer 69, 278-282), and even three-step nested (Funaki et al., (1997)Life Sciences 60, 643-652; Funaki et al., (1998) British Journal ofCancer 77, 1327-1332).

In one embodiment of the invention, separate enzymes are used forreverse transcription and PCR amplification. Two commonly used reversetranscriptases, for example, are avian myeloblastosis virus and Moloneymurine leukaemia virus. For amplification, a number of thermostableDNA-dependent DNA polymerases are currently available, although theydiffer in processivity, fidelity, thermal stability and ability to readmodified triphosphates such as deoxyuridine and deoxyinosine in thetemplate strand (Adams et al., (1994) Bioorganic and Medicinal Chemistry2, 659-667; Perler et al., (1996) Advances in Protein Chemistry 48,377-435). The most commonly used enzyme, Taq DNA polymerase, has a 5′-3′nuclease activity but lacks a 3′-5′ proofreading exonuclease activity.When fidelity is required, proofreading exonucleases such as Vent andDeep Vent (New England Biolabs) or Pfu (Stratagene) may be used (Clineet al., (1996) Nucleic Acids Research 24, 3456-3551). In anotherembodiment of the invention, a single enzyme approach may be usedinvolving a DNA polymerase with intrinsic reverse transcriptaseactivity, such as Thermus thermophius (Tth) polymerase (Bustin, (2000)Journal of Molecular Endocrinology 25, 169-193. A skilled artisan mayappreciate the variety of enzymes available for use in the presentinvention.

The methodologies and control gene primers of the present invention maybe used, for example, in any kinetic RT-PCR methodology, including thosethat combine fluorescence techniques with instrumentation capable ofcombining amplification, detection and quantification (Orlando et al.,(1998) Clinical Chemistry and Laboratory Medicine 36, 255-269). Thechoice of instrumentation is particularly important in multiplex RT-PCR,wherein multiple primer sets are used to amplify multiple specifictargets simultaneously. This requires simultaneous detection of multiplefluorescent dyes. Accurate quantitation while maintaining a broaddynamic range of sensitivity across mRNA levels is the focus of upcomingtechnologies, any of which are applicable for use in the presentinvention. Preferred instrumentation may be selected from the ABI Prism7700 (Perkin-Elmer-Applied Biosystems), the Lightcycler (Roche MolecularBiochemicals) and iCycler Thermal Cycler. Featured aspects of theseproducts include high-throughput capacities or unique photodetectiondevices.

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and the followingillustrative examples, practice the methods and use the control genes ofthe present invention. The following working examples therefore,specifically point out the preferred embodiments of the presentinvention, and are not to be construed as limiting in any way theremainder of the disclosure.

EXAMPLES Example 1 Selection of Control Genes

The control genes were selected by querying the Gene Logic GeneExpress®database to create expression profiles from a variety of human cell andtissue samples. Table 3 A-B lists and describes the tissue or cellsamples used to identify control genes listed in Tables 1 and 2. Thefirst column of Table 3 identifies the organ of the particular sample,the second details the morphology, and the third column provides thenumber of samples. Table 3 A-B includes 695 diseased and 560 normalsamples.

The GeneExpress® database was produced from data derived from screeningvarious cell or tissue samples using the Affymetrix human chip set. Ingeneral, tissue and cell samples were processed following the AffymetrixGeneChip® Expression Analysis Manual. Frozen tissue was first ground topowder using the Spex Certiprep 6800 Freezer Mill. Total RNA was thenextracted using Trizol (Invitrogen Life Technologies) followed by acleanup step utilizing the RNeasy Mini Kit and if required ethanolprecipitated to achieve a concentration of 1 μg/pl. Using 10-40 μg oftotal RNA, double stranded cDNA was created using the SuperScript Choicesystem (Invitrogen Life Technologies). First strand cDNA synthesis wasprimed with a T7-(dT₂₄) oligonucleotide. The cDNA was thenphenol-chloroform extracted and ethanol precipitated to a finalconcentration of 1 μg/μl.

55 μg of fragmented cRNA was hybridized on the Human Genome U95 set fortwenty-four hours at 60 rpm in a 45° C. hybridization oven, according tothe Affymetrix protocol. The chips were washed and stained withStreptavidin Phycoerythrin (SAPE) (Molecular Probes) in Affymetrixfluidics stations. To amplify staining, the chips were washed with SAPEsolution, stained with an anti-streptavidin biotinylated antibody(Vector Laboratories) followed by washing with SAPE solution.Hybridization to the probe arrays was detected by fluorometric scanning(Hewlett Packard Gene Array Scanner). Following hybridization andscanning, the microarray images were analyzed for quality control,looking for major chip defects or abnormalities in hybridization signal.After all chips passed quality control, the data was analyzed usingAffymetrix GeneChip® software (v3.0).

Gene expression data was then analyzed to identify those genes that areconsistently expressed across 1255 normal and disease samples, e.g.being called Present more than 95% of the time. Table 1 provides aninitial list of approximately 560 genes with a % CV less than 30% acrossthe normal and disease samples studied. Table 1 also provides the meanexpression value, an exemplary GenBank accession number for each of thegenes and the standard deviation value from the mean for each gene. TheGenBank accession numbers can be used to locate the publicly availablesequences and all GenBank accession numbers herein reported atspecifically incorporated by reference in their entirety. This list of560 genes from 1255 normal and diseased samples had been scanned onAffymetrix human U95 A GeneChip® scanned on a high photomultiplier tube(PMT) settings.

The gene list of Table 1 was then re-examined by utilizing human samplesrun on the Affyymetrix human U95 A GeneChip® scanned on a lowphotomultiplier tube (PMT) settings. The human samples consisted of 55human tissue samples and 46 human cancer cell lines. For each of thesesamples, the mean average difference, standard deviation and % CV weredetermined for each Affymetrix fragment on the human U95 A GeneChip®.The data was sorted by % CV and those gene fragments with values lessthan 40% were chosen for fiuther analysis after all genes withunderscore annotations were deleted (i.e. _f, _s, _r, etc.) [seewww.affimetrix.com].

The high PMT list was then compared with the low PMT list and all genesthat were not present on both lists were removed. All genes withunderscore annotations were then deleted from the list (i.e. _f, _s, _r,etc.). This resulted in a list of 771 genes. The list was then filteredto show CV values equal or less than 28% at low PMT settings as well asCV values equal or less than 31% at high PMT settings. Six additionalhuman genes with CV values equal or less 37% at low PMT settings andequal or less than 32% at high PMT settings were added to the list.These six genes have rat homologue genes that exhibited constant geneexpression over untreated and toxin treated rat samples scanned at lowPMT settings (˜200 samples). The resulting control gene list is in Table2.

Example 2 Quantitative PCR Analysis of Expression Levels Using theControl Genes

The expression levels of one or more genes listed in Tables 1 and 2 maybe used to normalize gene expression data produced using QuantitativePCR analysis. For example, Table 4 provides sequences for use as Taqmanprobes along with the forward and reverse primers for three genes:sorting nexin 3, polymerase (RNA) II (DNA directed) polypeptide F, andseryl-tRNA synthetase in Table 1 or 2. Real time PCR detection may beaccomplished by the use of the ABI PRISM 7700 Sequence Detection System.The 7700 measures the fluorescence intensity of the sample each cycleand is able to detect the presence of specific amplicons within the PCRreaction. TaqMan® assay provided by Perkin Ebner may be used to assayquantities of RNA. The primers may be designed from each of theidentified genes of Table 1 using Primer Express, a program developed byPE to efficiently find primers and probes for specific sequences. Theseprimers may be used in conjunction with SYBR green (Molecular Probes), anonspecific double stranded DNA dye, to measure the expression levelmRNA corresponding to the expression levels of each gene. This geneexpression data may then be used to normalize gene expression data ofother test genes.

Although the present invention has been described in detail withreference to examples above, it is understood that various modificationscan be made without departing from the spirit of the invention.Accordingly, the invention is limited only by the following claims. Allcited patents and publications referred to in this application areherein incorporated by reference in their entirety. TABLE 1 Expressionvalue Mean Std_dev Fragment No. Gene Name GenBank No. (overall)(overall) CV % 41785_at eukaryotic translation initiation factor 4gamma| 2 U73824 1825.59 392.92 21.52 34392_s_at RAB1| member RASoncogene family AL050268 1493.57 315.17 21.10 41194_at signalrecognition particle 14 kD (homologous Alu RNA-binding AI525652 1472.21312.41 21.22 protein) 41185_f_at SMT3 (suppressor of mif two 3| yeast)homolog 2 AI971724 1422.18 305.74 21.50 41833_at jumping translocationbreakpoint AB016492 1199.41 259.92 21.67 1394_at ras homolog genefamily| member A L25080 1031.88 223.38 21.65 38974_at RNA-bindingprotein regulatory subunit AF021819 910.49 199.88 21.95 505_at CDC37(cell division cycle 37| S. cerevisiae| homolog) U43077 628.94 137.4621.86 34849_at seryl-tRNA synthetase X91257 460.23 99.39 21.60 36942_atKIAA0174 gene product D79996 447.67 97.97 21.88 39811_at hypotheticalprotein MGC2749 AA402538 400.76 85.04 21.22 36110_at RAB5A| member RASoncogene family M28215 389.74 82.31 21.12 40819_at RNA binding motifprotein 8A AA161065 372.82 81.38 21.83 38672_at protein phosphatase 1|regulatory subunit 10 Y13247 249.96 53.96 21.59 33778_at chromosome 22open reading frame 4 AL096779 223.74 48.47 21.66 911_s_at calmodulin 2(phosphorylase kinase| delta) M19311 2123.80 478.30 22.52 37448_s_atguanine nucleotide binding protein (G protein)| alpha stimulating X560091544.74 354.90 22.97 activity polypeptide 1|neuroendocrine secretoryprotein 55 40864_at ras-related C3 botulinum toxin substrate 1 (rhofamily| small GTP D25274 1068.49 239.65 22.43 binding protein Rac1)41187_at death-associated protein 6 U26162 1052.43 238.95 22.70 39360_atsorting nexin 3 AF034546 944.20 210.75 22.32 32175_at CDC10 (celldivision cycle 10| S. cerevisiae| homolog) S72008 878.75 197.97 22.5332145_at adducin 1 (alpha) X58141 870.17 198.24 22.78 38831_f_at guaninenucleotide binding protein (G protein)| beta polypeptide 2 AF053356819.87 186.42 22.74 32766_at thyroid autoantigen 70 kD (Ku antigen)Z83840 804.64 180.45 22.43 35753_at U5 snRNP-specific protein (220 kD)|ortholog of S. cerevisiae Prp8p AB007510 704.30 156.01 22.15 36027_atpolymerase (RNA) II (DNA directed) polypeptide F AA418779 691.92 158.6522.93 38738_at SMT3 (suppressor of mif two 3| yeast) homolog 1 X99584642.57 144.63 22.51 38720_at chaperonin containing TCP1| subunit 7 (eta)AF026292 642.25 141.43 22.02 1695_at neural precursor cell expressed|developmentally down-regulated 8 D23662 620.09 141.48 22.82 38483_athypothetical protein AJ011916 605.91 135.19 22.31 38758_at PDGFAassociated protein 1 R98910 593.33 135.20 22.79 39782_at nuclearDNA-binding protein X95592 539.50 118.97 22.05 41132_r_at heterogeneousnuclear ribonucleoprotein H2 (H′) U01923 537.58 120.94 22.50 34864_athypothetical protein AF070638 528.37 117.67 22.27 35835_atanaphase-promoting complex subunit 5| periodontal ligament AB019409506.73 112.50 22.20 fibroblast protein 32575_at nucleosome assemblyprotein 1-like 4 U77456 466.80 103.15 22.10 38801_at VAMP(vesicle-associated membrane protein)-associated protein A AI742846451.66 101.60 22.50 (33 kD) 36611_at acid phosphatase 1| soluble U25849439.95 97.31 22.12 31826_at KIAA0674 protein AB014574 437.28 99.45 22.7439868_at poly(rC)-binding protein 3 AL046394 367.96 84.27 22.90 40824_atRAN binding protein 16 AB018288 340.15 77.74 22.85 33826_atCip1-interacting zinc finger protein AL120500 332.11 73.81 22.2337362_at RAB5B| member RAS oncogene family X54871 269.39 59.71 22.1640836_s_at metastasis-associated 1-like 1 W26677 217.72 47.91 22.0132820_at CCR4-NOT transcription complex| subunit 4 U71267 210.33 46.9122.30 35850_at phosphatidylserine receptor AI950382 173.78 39.77 22.8839136_at oxidative-stress responsive 1 AB017642 170.33 39.12 22.9741276_at sin3-associated polypeptide| 18 kD W27641 140.38 31.56 22.4836702_at T-box 19 AJ010277 135.27 31.04 22.94 37309_at ras homolog genefamily| member A L09159 2015.36 468.39 23.24 39740_g_atnascent-polypeptide-associated complex alpha polypeptide AF0541871774.49 419.00 23.61 35746_r_at poly(rC)-binding protein 2 X781361615.54 383.34 23.73 39758_f_at lysosomal-associated membrane protein 1J04182 1519.81 364.27 23.97 41221_at phosphoglycerate mutase 1 (brain)J04173 1508.34 355.87 23.59 1420_s_at eukaryotic translation initiationfactor 4A| isoform 2 D30655 1435.89 338.77 23.59 39415_at heterogeneousnuclear ribonucleoprotein K X72727 1361.71 317.49 23.32 40125_atcalnexin L10284 1244.21 293.89 23.62 32590_at nucleolin M60858 1156.35266.25 23.02 36972_at coated vesicle membrane protein X92098 1148.13268.13 23.35 35307_at GDP dissociation inhibitor 2 Y13286 1002.33 230.9523.04 324_f_at EST HG1515-HT1515 1001.35 232.80 23.25 880_atFK506-binding protein 1A (12 kD) M34539 887.82 205.06 23.10 41295_atGTT1 protein AL041780 878.34 203.61 23.18 37040_at KIAA0088 proteinD42041 826.78 194.69 23.55 723_s_at heterogeneous nuclearribonucleoprotein C (C1/C2) HG1322-HT5143 744.87 172.78 23.20 39184_attranscription elongation factor B (SIII)| polypeptide 2 (18 kD| elonginB) AI857469 734.63 173.55 23.62 34336_at lysyl-tRNA synthetase D32053705.01 162.51 23.05 41269_r_at API5-like 1 Y15906 680.76 162.93 23.9333341_at guanine nucleotide binding protein (G protein)| betapolypeptide 1 X04526 650.30 150.09 23.08 1311_at proteasome (prosome|macropain) subunit| beta type| 4 D26600 619.24 143.61 23.19 410_s_atcasein kinase 2| beta polypeptide X57152 613.46 141.25 23.03 34402_atunr-interacting protein AB024327 603.22 142.42 23.61 36949_at caseinkinase 1| delta U29171 546.48 130.09 23.81 941_at proteasome (prosome|macropain) subunit| beta type| 6 D29012 542.60 126.93 23.39 33397_atCDP-diacylglycerol-inositol 3-phosphatidyltransferase AL050383 480.14113.09 23.55 (phosphatidylinositol synthase) 39778_at mannosyl(alpha-1|3-)-glycoprotein beta-1|2-N- M55621 474.90 111.56 23.49acetylglucosaminyltransferase 38710_at hypothetical protein FLJ20113AL096714 456.86 105.09 23.00 33215_g_at mitochondrial ribosomal proteinS12 Y11681 439.32 103.28 23.51 33388_at EST AL080223 436.00 102.58 23.5338016_at heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-M94630 409.89 96.46 23.53 binding protein 1| 37 kD) 632_at glycogensynthase kinase 3 alpha L40027 373.13 88.22 23.64 34346_at proteinkinase| AMP-activated| gamma 1 non-catalytic subunit U42412 362.28 83.9423.17 41597_s_at SEC22| vesicle trafficking protein (S. cerevisiae)-like1 AF047442 307.93 72.68 23.60 1874_at RAD23 (S. cerevisiae) homolog BD21090 292.62 69.19 23.64 39047_at KIAA0156 gene product AB020880 277.7366.29 23.87 36574_at isocitrate dehydrogenase 3 (NAD+) gamma Z68907275.63 63.80 23.15 39164_at ariadne (Drosophila) homolog 2 AF099149225.58 52.80 23.41 41727_at KIAA1007 protein AB023224 153.39 36.64 23.8941483_s_at jun D proto-oncogene X56681 2091.94 520.54 24.88 38542_atnucleophosmin (nucleolar phosphoprotein B23| numatrin) U89322 1801.84448.04 24.87 1180_g_at heat shock 70 kD protein 8 HG2855-HT2995 1774.59428.21 24.13 35055_at basic transcription factor 3 X53281 1657.93 403.1524.32 254_at H3 histone| family 3A M11353 1590.81 382.95 24.0732316_s_at heat shock 90 kD protein 1| alpha X15183 1482.06 365.51 24.6639025_at 6.2 kd protein AI557912 1345.64 334.33 24.85 33458_r_at H2Bhistone family| member L AI688098 1220.62 297.73 24.39 36994_at ATPase|H+ transporting| lysosomal (vacuolar proton pump) 16 kD M62762 1072.06262.59 24.49 409_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenaseactivation X56468 983.68 241.73 24.57 protein| theta polypeptide33987_at ADP-ribosylation factor 1 M36340 968.58 233.00 24.06 1268_atubiquitin-activating enzyme E1 (A1S9T and BN75 temperature M58028 897.16219.32 24.45 sensitivity complementing) 37012_at capping protein (actinfilament) muscle Z-line| beta U03271 812.51 195.70 24.09 39030_at Rabacceptor 1 (prenylated) AJ133534 800.58 194.20 24.26 39866_at ubiquitinspecific protease 22 AB028986 789.47 194.01 24.57 36186_at RNA-bindingprotein S1| serine-rich domain L37368 766.92 190.58 24.85 35754_at ESTL40391 740.40 178.58 24.12 33666_at heterogeneous nuclearribonucleoprotein C (C1/C2) M16342 683.81 170.55 24.94 36517_at U2(RNU2)small nuclear RNA auxillary factor 1 (non-standard M96982 666.76 165.2524.78 symbol) 40189_at SET translocation (myeloid leukemia-associated)M93651 658.30 158.80 24.12 33875_at ATPase| H+ transporting| lysosomal(vacuolar proton pump) 9 kD AI547262 656.69 162.39 24.73 41224_atKIAA0788 protein AB018331 622.29 154.12 24.77 41241_at asparaginyl-tRNAsynthetase D84273 608.42 151.24 24.86 38413_at defender against celldeath 1 D15057 554.80 136.87 24.67 33198_at binder of Arl Two AA206524544.09 135.81 24.96 41309_g_at C-terminal binding protein 1 U37408537.50 132.44 24.64 1295_at v-rel avian reticuloendotheliosis viraloncogene homolog A (nuclear L19067 527.61 127.46 24.16 factor of kappalight polypeptide gene enhancer in B-cells 3 (p65)) 41830_at KIAA0494gene product AB007983 511.59 124.66 24.37 32241_at TAR DNA bindingprotein AL050265 510.14 127.08 24.91 34330_at cytochrome c oxidasesubunit VIIa polypeptide 2 like AB007618 499.29 121.64 24.36 41737_atSer/Arg-related nuclear matrix protein (plenty of prolines 101-like)AF048977 488.41 118.20 24.20 38297_at phosphatidylinositol transferprotein| membrane-associated X98654 463.69 112.50 24.26 457_s_atubiquitin-like 1 (sentrin) U67122 452.05 109.04 24.12 32832_atmacrophage erythroblast attacher AF084928 413.07 100.17 24.25 39147_g_atalpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. U72936385.04 95.45 24.79 cerevisiae) homolog) 38659_at suppressor of clear| C.elegans| homolog of AB020669 341.88 84.08 24.59 40988_at YME1 (S.cerevisiae)-like 1 AJ132637 341.77 82.87 24.25 38412_at proteinphosphatase 1| regulatory (inhibitor) subunit 11 U53588 336.42 81.3724.19 35790_at vacuolar protein sorting 26 (yeast homolog) AF054179328.77 80.27 24.42 35534_at KIAA0514 gene product AB011086 314.36 77.8324.76 36019_at serine/threonine kinase 19 L26260 310.58 76.38 24.5940130_at follistatin-like 1|hypothetical protein FLJ22169 U06863 298.8972.78 24.35 34906_g_at glutamate receptor, ionotropic, kainate 5AA977136 268.60 66.46 24.74 40404_s_at CDC16 (cell division cycle 16| S.cerevisiae| homolog) U18291 256.93 63.06 24.54 40426_at B-cellCLL/lymphoma 7B X89985 244.40 60.44 24.73 41540_at protein phosphatase1| regulatory subunit 7 Z50749 240.53 59.73 24.83 34231_at histoneacetyltransferase AF074606 237.47 59.16 24.91 36166_at splicing factorsimilar to dnaJ AF083190 226.95 55.72 24.55 36579_at ubiquitinationfactor E4A (homologous to yeast UFD2) D50916 225.21 56.06 24.89 1843_atEST HG2825-HT2949 220.98 55.23 24.99 41374_at ribosomal protein S6kinase| 70 kD| polypeptide 2 AB016869 217.24 54.19 24.94 33394_athypothetical protein FLJ11126 AA034074 212.62 51.45 24.20 40816_atnuclear phosphoprotein similar to S. cerevisiae PWP1 L07758 212.08 51.8624.45 36003_at poly(A)-specific ribonuclease (deadenylation nuclease)AJ005698 197.97 47.83 24.16 147_at tumor susceptibility gene 101 U82130190.90 47.73 25.00 32234_at dystonia 1| torsion (autosomal dominant;torsin A) AF007871 172.16 41.43 24.07 1612_s_at jun D proto-oncogeneX56681 2085.72 539.45 25.86 36587_at eukaryotic translation elongationfactor 2 Z11692 1910.61 487.20 25.50 31952_at ribosomal protein L6X69391 1813.14 468.79 25.86 33820_g_at lactate dehydrogenase B X137941781.14 453.34 25.45 31573_at ribosomal protein S25 M64716 1699.81438.15 25.78 31955_at Finkel-Biskis-Reilly murine sarcoma virus(FBR-MuSV) ubiquitously X65923 1620.25 408.37 25.20 expressed (foxderived); ribosomal protein S30 33943_at ferritin| heavy polypeptide 1L20941 1570.65 402.53 25.63 34891_at dynein| cytoplasmic| lightpolypeptide AI540958 1557.07 397.55 25.53 34646_at ribosomal protein S7Z25749 1458.01 366.55 25.14 33451_s_at ribosomal protein L22 AI5260791318.46 331.97 25.18 39019_at lysosomal-associated protein transmembrane4 alpha D14696 1285.43 328.63 25.57 40281_at neural precursor cellexpressed| developmentally down-regulated 5 D63878 1159.40 298.10 25.7141724_at accessory proteins BAP31/BAP29 X81817 1130.18 287.58 25.4536986_at lysophospholipase II AL031295 945.11 244.21 25.84 34877_atJanus kinase 1 (a protein tyrosine kinase) AL039831 920.60 236.94 25.7435787_at dynein| cytoplasmic| intermediate polypeptide 2 AI986201 919.87231.48 25.16 39003_at pituitary tumor-transforming 1 interacting proteinZ50022 915.25 235.56 25.74 36654_s_at heterogeneous nuclearribonucleoprotein A2/B1 M29065 900.89 230.63 25.60 35292_at HLA-Bassociated transcript-1 Z37166 815.55 210.60 25.82 38657_s_at clathrin|light polypeptide (Lca) M20471 804.86 208.87 25.95 32220_athigh-mobility group (nonhistone chromosomal) protein 1 D63874 756.62189.42 25.04 38663_at Breakpoint cluster region protein| uterineleiomyoma| 1; barrier to AI033692 730.14 188.61 25.83 autointegrationfactor 38733_at X-ray repair complementing defective repair in Chinesehamster cells M30938 699.28 175.17 25.05 5 (double-strand-breakrejoining; Ku autoantigen| 80 kD) 35749_at transcriptional adaptor 3(ADA3| yeast homolog)-like (PCAF histone AF069733 629.52 161.07 25.59acetylase complex) 223_at ubiquitin-conjugating enzyme E2L 3 S81003585.33 148.38 25.35 1499_at farnesyltransferase| CAAX box| alpha L10413576.15 146.04 25.35 35783_at vesicle-associated membrane protein 3(cellubrevin) H93123 532.51 133.72 25.11 35279_at Tax1 (human T-cellleukemia virus type I) binding protein 1 U33821 483.39 123.00 25.4540063_at nuclear domain 10 protein U22897 479.54 121.16 25.27 36645_atv-rel avian reticuloendotheliosis viral oncogene homolog A (nuclearL19067 467.83 119.55 25.55 factor of kappa light polypeptide geneenhancer in B-cells 3 (p65)) 37389_at small acidic protein AI346580456.73 116.38 25.48 36137_at chromodomain helicase DNA binding protein 4X86691 453.01 114.59 25.30 32836_at 1-acylglycerol-3-phosphateO-acyltransferase 1 (lysophosphatidic U56417 452.04 116.91 25.86 acidacyltransferase| alpha) 38450_at Sjogren syndrome antigen B (autoantigenLa) X69804 433.17 110.29 25.46 41366_at KIAA1002 protein AB023219 392.83101.32 25.79 37321_at tetratricopeptide repeat domain 1 U46570 378.2497.01 25.65 35359_at KIAA0235 protein D87078 356.06 90.11 25.31 41335_atDKFZP566O1646 protein AL050084 348.57 89.78 25.76 32586_at KIAA0217protein D86971 321.19 82.43 25.67 32591_at HCDI protein AI494623 310.7180.25 25.83 35187_at EST AL080216 307.74 77.04 25.04 39435_at prefoldin1 D45333 305.60 76.71 25.10 40414_at valyl-tRNA synthetase 2 X59303303.73 77.00 25.35 40469_at minichromosome maintenance deficient (S.cerevisiae) 3-associated AB011144 292.48 73.84 25.24 protein 36080_atclock (mouse) homolog AB002332 260.18 67.26 25.85 34370_at archain 1X81198 250.74 63.61 25.37 32039_at adaptor-related protein complex 3|beta 1 subunit U81504 233.73 59.69 25.54 40849_s_at cAMP responsiveelement binding protein 3 (luman) U88528 229.61 57.97 25.25 33861_atCCR4-NOT transcription complex| subunit 2 AI123426 211.54 54.09 25.5736603_at GCN1 (general control of amino-acid synthesis 1| yeast)-likeD86973 199.11 50.97 25.60 1| homeodomain-interacting protein kinase 240052_at ARP1 (actin-related protein 1| yeast) homolog A (centractinalpha) X82206 185.41 47.96 25.87 314_at phosphatidylinositol glycan|class B D42138 183.52 46.89 25.55 31860_at putative receptor proteinX51804 151.68 38.76 25.56 32713_at golgi autoantigen| golgin subfamilya| 1 U51587 147.24 38.12 25.89 35743_at cleavage and polyadenylationspecific factor 4| 30 kD subunit U79569 128.76 33.05 25.67 31708_atribosomal protein L30 L05095 2416.22 650.09 26.91 32315_at ribosomalprotein S24 M31520 2358.55 632.51 26.82 327_f_at EST HG1800-HT18232348.03 625.69 26.65 36333_at ribosomal protein L7 X57958 2277.08 599.7626.34 33677_at ribosomal protein L24 M94314 2153.43 571.37 26.5333657_at ribosomal protein L34 L38941 2146.73 566.47 26.39 32487_s_atkaryopherin alpha 4 (importin alpha 3)|ribosomal protein| large P2AB002533 2119.07 567.25 26.77 33660_at ribosomal protein L5 U149662010.05 527.61 26.25 39830_at ribosomal protein L27 AA044823 1990.00530.31 26.65 1367_f_at ubiquitin C M26880 1975.66 520.20 26.33 36795_atprosaposin (variant Gaucher disease and variant metachromatic J030771898.29 499.48 26.31 leukodystrophy) 41231_f_at high-mobility group(nonhistone chromosomal) protein 17 X13546 1850.84 490.00 26.47 33984_atheat shock 90 kD protein 1| beta M16660 1677.04 446.26 26.61 32394_s_atribosomal protein L23 X55954 1630.44 424.17 26.02 33485_at ribosomalprotein L4 D23660 1623.23 432.42 26.64 31907_at ribosomal protein L14D87735 1588.57 413.70 26.04 32272_at tubulin| alpha| ubiquitous K005581519.01 408.21 26.87 34381_at cytochrome c oxidase subunit VIIc AI7088891483.67 395.32 26.64 41256_at eukaryotic translation elongation factor 1delta (guanine nucleotide Z21507 1328.54 348.13 26.20 exchange protein)41768_at protein kinase| cAMP-dependent| regulatory| type 1| alpha(tissue M33336 1302.05 349.10 26.81 specific extinguisher 1) 1009_athistidine triad nucleotide-binding protein U51004 1133.18 301.26 26.5939856_at ribosomal protein L36a AI708983 1124.95 298.25 26.51 36138_atcalpain 4| small subunit (30K) X04106 1011.52 270.95 26.79 40637_at heatshock 70 kD protein 8 Y00371 996.35 262.73 26.37 38527_atnon-POU-domain-containing| octamer-binding U02493 944.25 254.22 26.9237364_at B-cell associated protein U72511 894.01 235.05 26.29 39800_s_atHS1 binding protein U68566 816.62 213.20 26.11 39336_at ADP-ribosylationfactor 3 M74491 717.23 189.84 26.47 32530_at tyrosine3-monooxygenase/tryptophan 5-monooxygenase activation X56468 698.12184.17 26.38 protein| theta polypeptide 905_at guanylate kinase 1 L76200678.74 181.25 26.70 838_s_at ubiquitin-conjugating enzyme E2I(homologous to yeast UBC9) U45328 662.09 176.95 26.73 33154_atproteasome (prosome| macropain) subunit| beta type| 4 D26600 658.73174.10 26.43 688_at proteasome (prosome| macropain) 26S subunit| ATPase|1 L02426 651.35 169.84 26.07 35316_at Ras-related GTP-binding proteinU41654 634.52 171.30 27.00 31906_at heat shock factor binding protein 1AF068754 632.01 166.68 26.37 1450_g_at proteasome (prosome| macropain)subunit| alpha type| 4 D00763 602.83 160.76 26.67 1641_s_atdamage-specific DNA binding protein 1 (127 kD) U32986 585.59 155.1026.49 39079_at enhancer of rudimentary (Drosophila) homolog D85758574.87 154.61 26.89 35302_at nuclear RNA export factor 1 AJ132712 530.82139.38 26.26 37395_at ATPase| vacuolar| 14 kD D49400 521.98 136.38 26.131158_s_at calmodulin 3 (phosphorylase kinase| delta) J04046 515.17138.95 26.97 39346_at GAP-associated tyrosine phosphoprotein p62 (Sam68)M88108 506.62 133.58 26.37 868_at TATA box binding protein(TBP)-associated factor| RNA polymerase U13991 495.16 131.44 26.54 II|H| 30 kD 37367_at ATPase| H+ transporting| lysosomal (vacuolar protonpump) 31 kD X76228 491.45 130.10 26.47 498_at Tax1 (human T-cellleukemia virus type I) binding protein 1 U33821 482.31 128.42 26.6336571_at topoisomerase (DNA) II beta (180 kD) X68060 471.68 123.52 26.1937719_at myeloid leukemia factor 2 AF070539 468.02 123.95 26.48 35337_atF-box only protein 7 AL050254 442.72 116.37 26.28 41170_at KIAA0663 geneproduct AB014563 406.22 106.10 26.12 33818_at valosin-containing proteinAC004472 396.96 104.80 26.40 34773_at tubulin-specific chaperone aAF038952 374.99 100.24 26.73 41413_at cleft lip and palate associatedtransmembrane protein 1 AF037339 362.49 94.27 26.01 37336_at UBXdomain-containing 1 D87684 337.75 89.52 26.51 35826_at suppressor of Ty(S. cerevisiae) 5 homolog AF040253 335.01 89.78 26.80 37031_at C9orf10protein D80005 332.88 89.07 26.76 37010_at general transcription factorIIA| 2 (12 kD subunit) AI203737 330.68 87.21 26.37 40048_at KIAA0099gene product D43951 313.60 84.42 26.92 41606_at developmentallyregulated GTP-binding protein 1 AJ005940 310.48 83.31 26.83 34089_atKIAA1030 protein AB028953 305.13 80.75 26.46 155_s_at ubiquitin-like 1(sentrin) U61397 301.59 78.76 26.12 37928_at nuclear transcriptionfactor Y| beta AA621555 294.85 76.93 26.09 1119_at replication proteinA2 (32 kD) J05249 287.23 76.53 26.65 38809_s_at exostoses(multiple)-like 3 AB011091 284.07 74.72 26.30 35750_at uncharacterizedhypothalamus protein HT010 AL049948 281.29 73.86 26.26 39723_at cullin 1AF062536 266.89 71.32 26.72 32171_at eukaryotic translation initiationfactor 5 AL080102 264.68 69.05 26.09 35353_at proteasome (prosome|macropain) 26S subunit| ATPase| 2 D11094 261.18 69.75 26.71 41151_atSKIP for skeletal muscle and kidney enriched inositol phosphatase U45973254.76 68.53 26.90 452_at SWI/SNF related| matrix associated| actindependent regulator of U66615 251.78 66.11 26.26 chromatin| subfamily c|member 1 40160_at KIAA0618 gene product AL080109 251.72 66.68 26.4938093_at CGI-35 protein U90909 250.92 67.43 26.87 32658_at SAC2suppressor of actin mutations 2-like (yeast) AL031228 248.89 66.05 26.5437737_at protein-L-isoaspartate (D-aspartate) O-methyltransferase D25547241.91 65.11 26.91 32592_at KIAA0323 protein AB002321 239.55 64.28 26.8335244_at KIAA0460 protein AB007929 200.99 53.83 26.78 37390_at pre-mRNAsplicing factor similar to S. cerevisiae Prp16 D86977 176.59 47.50 26.901711_at tumor protein p53-binding protein| 1 U09477 166.58 43.59 26.1737609_at nucleotide binding protein 1 (E. coli MinD like) U01833 116.3131.25 26.87 35125_at ribosomal protein S6 X67309 2371.33 654.78 27.611676_s_at eukaryotic translation elongation factor 1 gamma M554092315.63 639.50 27.62 1653_at ribosomal protein S3A M84711 2275.89 629.8727.68 1323_at ubiquitin B X04803 2199.84 599.98 27.27 32153_s_atubiquitin B U49869 2155.85 584.70 27.12 34644_at beta-2-microglobulinAB021288 2144.72 595.49 27.77 41206_r_at cytochrome c oxidase subunitVIa polypeptide 1 AI540925 2133.29 582.59 27.31 32440_at ribosomalprotein L17 X53777 2071.48 570.77 27.55 39739_atnascent-polypeptide-associated complex alpha polypeptide AF0541872019.90 554.73 27.46 34570_at ribosomal protein S27a S79522 1941.41542.32 27.93 31538_at ribosomal protein| large| P0 M17885 1935.63 541.2827.96 37450_r_at guanine nucleotide binding protein (G protein)| alphastimulating X04409 1931.64 523.01 27.08 activity polypeptide1|neuroendocrine secretory protein 55 31509_at ribosomal protein L13X64707 1893.41 517.78 27.35 32337_at ribosomal protein L21 (gene orpseudogene) U25789 1824.69 495.86 27.17 41152_f_at ribosomal protein L44T89651 1734.56 485.33 27.98 34609_g_at guanine nucleotide bindingprotein (G protein)| beta polypeptide 2-like 1 M24194 1733.33 479.5127.66 37677_at phosphoglycerate kinase 1 V00572 1525.89 417.32 27.351836_at cyclin| D50310 1498.70 412.79 27.54 33619_at ribosomal proteinS13 L01124 1395.71 390.29 27.96 39738_at EST Z82215 1392.97 382.38 27.4541213_at peroxiredoxin 1 X67951 1368.15 380.40 27.80 41765_at ribosomalprotein L35 AI541285 1334.55 364.70 27.33 37720_at heat shock 60 kDprotein 1 (chaperonin) M22382 1265.49 353.60 27.94 1179_at ESTHG2855-HT2995 1261.82 345.61 27.39 35745_f_at poly(rC)-binding protein 2X78136 1208.03 333.10 27.57 40436_g_at solute carrier family 25(mitochondrial carrier; adenine nucleotide J03592 1074.34 291.35 27.12translocator)| member 6 970_r_at ubiquitin specific protease 9| Xchromosome (Drosophila fat facets X98296 953.52 264.06 27.69 related)35363_at DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72 kD)AL080113 946.56 263.90 27.88 36147_at signal sequence receptor| beta(translocon-associated protein beta) X74104 836.90 233.12 27.86 35298_ateukaryotic translation initiation factor 3| subunit 7 (zeta| 66/67 kD)U54558 826.39 230.28 27.87 39127_f_at protein phosphatase 2A| regulatorysubunit B′ (PR 53) X73478 817.98 228.78 27.97 38084_at chromobox homolog3 (Drosophila HP1 gamma) AA648295 809.23 222.77 27.53 36111_s_athypothetical protein ET| splicing factor| arginine/serine-rich 2 X75755779.82 210.62 27.01 38110_at syndecan binding protein (syntenin)AF000652 761.28 212.10 27.86 36928_at zinc finger protein 146 X70394728.32 198.65 27.27 32573_at splicing factor| arginine/serine-rich 9AL021546 722.59 200.04 27.68 162_at ubiquitin specific protease 11U44839 717.68 194.67 27.13 36152_at GDP dissociation inhibitor 1 X79353681.78 187.98 27.57 36981_at signal recognition particle 9 kD AF070649681.11 186.36 27.36 35336_at EST AL021707 628.65 174.85 27.81 38736_atWD repeat domain 1 AL050108 608.50 165.27 27.16 37346_atADP-ribosylation factor 5 M57567 600.57 167.03 27.81 36991_at splicingfactor| arginine/serine-rich 4 L14076 565.58 156.93 27.75 34393_r_atRAB1| member RAS oncogene family AL050268 527.91 142.62 27.02 36187_atribonuclease/angiogenin inhibitor X13973 520.02 143.17 27.53 36035_atanchor attachment protein 1 (Gaa1p| yeast) homolog AB002135 518.45142.81 27.55 31893_at ADP-ribosylation factor-like 2 L13687 511.24140.35 27.45 37730_at EBNA-2 co-activator (100 kD) U22055 499.00 137.7627.61 37717_at heterogeneous nuclear ribonucleoprotein M L03532 489.66135.30 27.63 40791_at polymerase (RNA) II (DNA directed) polypeptide A(220 kD) X63564 487.70 135.64 27.81 38990_at F-box only protein 9AL031178 483.87 130.86 27.04 37666_at proteasome (prosome| macropain)subunit| beta type| 5 D29011 466.82 126.17 27.03 38074_atadaptor-related protein complex 3| sigma 1 subunit U91932 458.09 127.3727.80 2093_s_at X-ray repair complementing defective repair in Chinesehamster cells J04977 456.87 123.57 27.05 5 (double-strand-breakrejoining; Ku autoantigen| 80 kD) 1707_g_at v-raf murine sarcoma 3611viral oncogene homolog 1 U01337 451.30 123.34 27.33 38050_at KIAA0164gene product D79986 427.55 118.37 27.69 33770_at conservedhelix-loop-helix ubiquitous kinase AF009225 389.91 105.78 27.13 584_s_atX-ray repair complementing defective repair in Chinese hamster cellsM30938 367.41 100.27 27.29 5 (double-strand-break rejoining; Kuautoantigen| 80 kD) 33860_at KIAA0462 protein AB007931 366.96 102.3927.90 37318_at eukaryotic translation termination factor 1 X81625 365.75101.16 27.66 34680_s_at KIAA0107 gene product D14663 362.96 100.09 27.5838713_at EST Z99716 361.32 98.49 27.26 41267_at KIAA1049 proteinAB028972 357.38 97.24 27.21 32572_at ubiquitin specific protease 9| Xchromosome (Drosophila fat facets X98296 332.71 90.61 27.23 related)34374_g_at upstream regulatory element binding protein 1 Z97054 321.1188.15 27.45 39711_at protein kinase C substrate 80K-H J03075 319.6087.78 27.47 35268_at hypothetical protein DKFZp586F1122 similar toaxotrophin AL050171 313.65 87.38 27.86 35653_at G protein pathwaysuppressor 2 U28963 310.61 85.73 27.60 34326_at coatomer proteincomplex| subunit beta X82103 308.28 84.76 27.49 641_at presenilin 1(Alzheimer disease 3) L76517 306.24 85.17 27.81 38993_r_at EST W27522291.43 79.75 27.36 36971_at KIAA0257 protein D87446 278.89 77.69 27.86421_at translocated promoter region (to activated MET oncogene) X66397258.24 71.72 27.77 39108_at lanosterol synthase(2|3-oxidosqualene-lanosterol cyclase) U22526 254.13 69.15 27.2135987_g_at member of MYST family histone acetyl transferases| homolog ofAL050395 238.29 65.51 27.49 Drosophila MOF 41800_s_at tetratricopeptiderepeat domain 2 U46571 234.15 65.39 27.93 36463_at BCL2-associatedathanogene 5 AB020680 230.63 62.39 27.05 40169_at cargo selectionprotein (mannose 6 phosphate receptor binding AF057140 219.28 60.4027.54 protein) 32594_at aspartylglucosaminidase| chaperonin containingTCP1| subunit 4 AF026291 214.02 57.89 27.05 (delta) 237_s_at proteinphosphatase 2 (formerly 2A)| catalytic subunit| alpha isoform M60483207.99 56.46 27.15 39659_at Ts translation elongation factor|mitochondrial L37936 195.72 53.60 27.38 39083_at ubiquitin-conjugatingenzyme E2D 3 (homologous to yeast UBC4/5) U39318 185.17 51.55 27.841885_at excision repair cross-complementing rodent repair deficiency|M31899 179.82 48.99 27.24 complementation group 3 (xeroderma pigmentosumgroup B complementing) 35166_at Down syndrome critical region gene 3D87343 154.33 41.98 27.20 31829_r_at trans-Golgi network protein (46|48| 51 kD isoforms) AF027515 147.16 41.05 27.90 41063_g_at meningiomaexpressed antigen 5 (hyaluronidase) AA037278 139.74 39.09 27.9738899_s_at hypothetical protein FLJ20693 U95822 134.53 37.33 27.7540886_at PRO2047 protein| eukaryotic translation elongation factor 1alpha 1- L41498 2553.34 716.99 28.08 like 14 37449_i_at guaninenucleotide binding protein (G protein)| alpha stimulating X04409 2542.93727.52 28.61 activity polypeptide 1 32334_f_at ubiquitin C AB0090102484.94 698.40 28.11 36358_at ribosomal protein L9 U09953 2319.22 664.4728.65 41178_at ribosomal protein L11 X79234 2308.70 647.00 28.0233667_at peptidylprolyl isomerase A (cyclophilin A) X52851 2299.52654.15 28.45 1315_at omithine decarboxylase antizyme 1 D78361 2286.84658.74 28.81 32435_at ribosomal protein L19 X63527 2284.19 646.33 28.3032437_at ribosomal protein S5 U14970 2225.71 640.95 28.80 32341_f_atribosomal protein L23a U37230 2137.05 608.03 28.45 33614_at ribosomalprotein L18a X80822 2104.73 609.73 28.97 34608_at guanine nucleotidebinding protein (G protein)| beta polypeptide 2-like 1 M24194 2100.39601.81 28.65 41741_at RNA binding motif protein 3 U28686 2093.05 597.3528.54 33659_at cofilin 1 (non-muscle) X95404 1893.82 531.98 28.0931546_at ribosomal protein L18 L11566 1779.05 510.46 28.69 32432_f_atribosomal protein L15 L25899 1729.12 501.16 28.98 31584_at tumorprotein| translationally-controlled 1 X16064 1723.64 485.94 28.191161_at heat shock 90 kD protein 1| beta J04988 1508.47 430.13 28.511980_s_at non-metastatic cells 2| protein (NM23B) expressed in X589651466.91 416.32 28.38 38708_at RAN| member RAS oncogene family AF0541831453.07 410.77 28.27 32340_s_at nuclease sensitive element bindingprotein 1 M85234 1379.82 391.42 28.37 36668_at diaphorase (NADH)(cytochrome b-5 reductase) M28713 1361.73 389.25 28.59 37003_at CD63antigen (melanoma 1 antigen) X62654 1321.50 378.24 28.62 38590_r_atprothymosin| alpha (gene sequence 28) M14630 1319.89 372.46 28.221424_s_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activationD78577 1319.87 376.56 28.53 protein| eta polypeptide 1235_at tyrosine3-monooxygenase/tryptophan 5-monooxygenase activation M86400 1317.80376.87 28.60 protein| zeta polypeptide 37675_at solute carrier family 25(mitochondrial carrier; phosphate carrier)| X60036 1270.20 360.95 28.42member 3 39921_at cytochrome c oxidase subunit Vb AI526089 1230.78345.45 28.07 32166_at KIAA1027 protein|talin AB028950 1196.59 342.8728.65 38485_at NADH dehydrogenase (ubiquinone) 1| subcomplex unknown| 1(6 kD| AA760866 1186.58 343.63 28.96 KFYI) 40777_at catenin(cadherin-associated protein)| beta 1 (88 kD) X87838 1009.82 284.2928.15 35747_at stromal cell derived factor receptor 1 AF035287 990.74279.13 28.17 38479_at acidic protein rich in leucines Y07969 988.91282.66 28.58 1817_at prefoldin 5 D89667 963.78 274.72 28.50 40875_s_atsmall nuclear ribonucleoprotein 70 kD polypeptide (RNP antigen) X06815929.39 260.44 28.02 40134_at ATP synthase| H+ transporting|mitochondrial F0 complex| subunit f| AF047436 899.04 253.99 28.25isoform 2 1199_at eukaryotic translation initiation factor 4A| isoform 1D13748 892.85 253.08 28.35 32576_at eukaryotic translation initiationfactor 3| subunit 5 (epsilon| 47 kD) U94855 843.99 238.11 28.21 40898_atsequestosome 1 U46751 831.41 238.14 28.64 35767_at gangliosideexpression factor 2 AI565760 783.62 223.09 28.47 922_at proteinphosphatase 2 (formerly 2A)| regulatory subunit A (PR 65)| J02902 780.98222.67 28.51 alpha isoform 35770_at ATPase| H+ transporting| lysosomal(vacuolar proton pump)| subunit 1 D16469 774.14 217.42 28.09 39867_at Tutranslation elongation factor| mitochondrial S75463 737.22 210.58 28.5638779_r_at hepatoma-derived growth factor (high-mobility group protein1-like) D16431 733.82 207.97 28.34 38480_s_at ubiquitin-conjugatingenzyme E2I (homologous to yeast UBC9) U66867 725.16 207.77 28.6540874_at endothelial differentiation-related factor 1 AJ005259 686.91197.37 28.73 32408_s_at EST AL022101 686.55 193.43 28.17 36950_at gp25L2protein|sulfotransferase family| cytosolic| 1C| member 2 X90872 652.46184.68 28.30 41268_g_at KIAA1049 protein AB028972 645.47 187.01 28.9731932_f_at basic transcription factor 3 M90357 635.47 178.99 28.171310_at proteasome (prosome| macropain) subunit| beta type| 2 D26599632.60 179.78 28.42 33443_at EST Z99129 583.58 167.76 28.75 38814_atATPase| H+ transporting| lysosomal (vacuolar proton pump)| member JAF038954 565.80 163.29 28.86 34305_at poly(rC)-binding protein 1 Z29505560.63 158.60 28.29 34338_at cytoskeleton-associated protein 1 D49738557.85 160.89 28.84 37569_at programmed cell death 6 AF035606 557.03160.99 28.90 38778_at KIAA1046 protein AB028969 556.85 158.44 28.451728_at murine leukemia viral (bmi-1) oncogene homolog L13689 541.21156.14 28.85 32803_at cornichon-like AF104398 536.76 153.44 28.5937729_at exportin 1 (CRM1| yeast| homolog) Y08614 523.31 151.12 28.88585_at X-ray repair complementing defective repair in Chinese hamstercells M30938 522.85 150.23 28.73 5 (double-strand-break rejoining; Kuautoantigen| 80 kD) 882_at colony stimulating factor 1 (macrophage)M37435 511.72 143.88 28.12 39370_at Microtubule-associated proteins 1Aand 1B| light chain 3 W28807 507.65 143.26 28.22 41212_r_atWilliams-Beuren syndrome chromosome region 1 D26068 488.87 137.63 28.1533877_s_at KIAA1067 protein AB028990 486.65 136.63 28.07 1446_atproteasome (prosome| macropain) subunit| alpha type| 2 D00760 472.98133.17 28.16 41197_at RAD23 (S. cerevisiae) homolog A D21235 459.28132.47 28.84 37300_at dynein| cytoplasmic| heavy polypeptide 1 AB002323446.27 126.74 28.40 1030_s_at topoisomerase (DNA)| U07806 444.60 128.7228.95 38282_at a disintegrin and metalloproteinase domain 15(metargidin) U41767 424.89 120.16 28.28 32569_at platelet-activatingfactor acetylhydrolase| isoform lb| alpha subunit L13385 424.73 119.9328.24 (45 kD) 36845_at KIAA0136 protein D50926 401.91 115.00 28.6132853_at translocase of outer mitochondrial membrane 70 (yeast) homologA AB018262 388.05 111.34 28.69 37860_at DKFZP564F1422 protein AL049942379.05 107.48 28.35 32209_at Mouse Mammary Turmor Virus Receptor homologAF052151 374.27 105.88 28.29 39029_at matemal G10 transcript U11861368.78 106.14 28.78 1313_at proteasome (prosome| macropain) subunit|beta type| 7 D38048 359.96 101.82 28.29 1398_g_at mitogen-activatedprotein kinase kinase kinase 11 L32976 351.84 100.27 28.50 35263_atglutathione S-transferase M1 N73769 350.90 100.48 28.64 37931_atcentromere protein B (80 kD) X05299 350.36 101.52 28.98 35836_at nucleardistribution gene C (A. nidulans) homolog AB019408 346.50 98.88 28.5433424_at ribophorin I Y00281 345.17 99.65 28.87 37670_at annexin A7J04543 339.52 96.40 28.39 869_at general transcription factor IIA| 2 (12kD subunit) U14193 325.31 93.67 28.80 32117_at apoptosis antagonizingtranscription factor U51698 316.94 90.54 28.57 41316_s_at scaffoldattachment factor B U72355 287.71 83.12 28.89 38705_atubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5) AI310002284.21 81.17 28.56 40615_at hypothetical protein FLJ21439 AA780049265.07 74.85 28.24 38475_at dynactin 2 (p50) U50733 260.78 74.16 28.44504_at ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)U39318 259.05 73.73 28.46 34692_r_at actin related protein 2/3 complex|subunit 4 (20 kD) AF006087 254.79 71.76 28.16 37703_at Rabgeranylgeranyltransferase| beta subunit Y08201 244.42 69.34 28.3741604_at EST U79297 241.37 68.58 28.41 32205_at protein kinase|interferon-inducible double stranded RNA dependent AF072860 241.35 68.8028.50 activator 37911_at syntaxin 4A (placental) U07158 238.94 68.9128.84 1074_at RAB1| member RAS oncogene family M28209 236.35 66.47 28.1241097_at telomeric repeat binding factor 2 AF002999 213.33 61.81 28.9839368_at eukaryotic translation initiation factor 2| subunit 2 (bete| 38kD) AL031668 209.73 59.84 28.53 39141_at ATP-binding cassette|sub-family F (GCN20)| member 1 AF027302 192.53 54.74 28.43 41699_f_atbromodomain-containing 1 AL080149 190.86 54.73 28.68 1453_at MAD(mothers against decapentaplegic| Drosophila) homolog 2 U68018 189.6953.39 28.15 34705_at similar to yeast BET3 (S. cerevisiae) AJ224335178.32 50.74 28.46 39342_at methionine-tRNA synthetase X94754 174.5750.36 28.85 35368_at zinc finger protein 207 AF046001 153.79 44.08 28.6733841_at hypothetical protein FLJ11560 R48209 140.73 39.88 28.3439403_at KIAA0678 protein AB014578 127.16 35.83 28.17 193_at TATA boxbinding protein (TBP)-associated factor| RNA polymerase U21858 124.4535.43 28.47 II| G| 32 kD 40537_at KIAA0741 gene product AB018284 119.0933.47 28.10 35286_r_at putative nucleic acid binding protein RY-1 X76302104.69 30.35 28.99 35119_at ribosomal protein L13a X56932 2374.45 697.6229.38 31568_at ribosomal protein S10 U14972 2240.21 649.67 29.0032330_at ribosomal protein S11 X06617 2087.27 608.76 29.17 34592_atribosomal protein S17 M13932 2041.57 595.03 29.15 32436_at ribosomalprotein L27a U14968 1911.48 560.72 29.33 33656_at ribosomal protein L37D23661 1861.14 549.25 29.51 33668_at ribosomal protein L12 AF0376431553.32 461.37 29.70 39798_at ribosomal protein S28 R87876 1506.80443.11 29.41 1718_at actin related protein 2/3 complex| subunit 2 (34kD) U50523 1429.15 418.75 29.30 37307_at guanine nucleotide bindingprotein (G protein)| alpha inhibiting activity X04828 1284.55 379.2529.52 polypeptide 2 39027_at cytochrome c oxidase subunit IV AF0171151271.56 372.18 29.27 955_at EST HG1862-HT1897 977.60 283.88 29.0441220_at MLL septin-like fusion AB023208 960.99 279.78 29.11 38075_atsynaptophysin-like protein X68194 896.44 267.11 29.80 39033_atchromosome 1 open reading frame 8 Z78368 856.61 253.99 29.65 32324_attyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation X57346818.90 240.26 29.34 protein| beta polypeptide 40593_at polypyrimidinetract binding protein (heterogeneous nuclear X66975 803.31 239.11 29.77ribonucleoprotein I) 41235_at activating transcription factor 4(tax-responsive enhancer element AL022312 793.91 233.65 29.43 B67).32774_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex| 8 (19 kD|AI541050 731.80 215.75 29.48 ASHI) 31492_at muscle specific geneAB019392 684.80 202.42 29.56 41834_g_at jumping translocation breakpointAB016492 664.62 198.64 29.89 32335_r_at ubiquitin C AB009010 626.97185.42 29.57 41233_at MRJ gene for a member of the DNAJ protein familyAB014888 626.57 185.50 29.61 40783_s_at phosphatidylinositol 4-kinase|catalytic| alpha polypeptide L36151 623.93 184.30 29.54 34796_attranslocating chain-associating membrane protein X63679 610.94 177.9029.12 41202_s_at conserved gene amplified in osteosarcoma AF000152603.25 178.02 29.51 40867_at protein phosphatase 2 (formerly 2A)|regulatory subunit A (PR 65)| J02902 591.17 173.56 29.36 alpha isoform2050_s_at ras-related C3 botulinum toxin substrate 1 (rho family| smallGTP M29870 583.02 169.72 29.11 binding protein Rac1) 39363_at putativebreast adenocarcinoma marker (32 kD) AF042384 539.48 157.47 29.1934791_at t-complex 1 X52882 535.37 159.39 29.77 38375_at esteraseD/formylglutathione hydrolase AF112219 512.06 149.48 29.19 40467_atsuccinate dehydrogenase complex| subunit D| integral membrane AB006202511.52 149.42 29.21 protein 32478_f_at EST AL031133 504.81 146.84 29.0938690_at chromosome 3 open reading frame 4 AL080097 503.41 146.77 29.1540106_at E1B-55 kDa-associated protein 5 AJ007509 497.05 146.61 29.5037387_r_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum proteinretention X55885 469.97 139.61 29.71 receptor 1 40108_at KIAA0005 geneproduct D13630 429.34 127.15 29.61 32235_at KIAA0544 protein AB011116421.84 124.11 29.42 40546_s_at NADH dehydrogenase (ubiquinone) 1 alphasubcomplex| 2 (8 kD| B8) AF047185 415.67 122.99 29.59 41594_at Januskinase 1 (a protein tyrosine kinase) M64174 415.30 122.67 29.54 35983_atEST AC004528 409.89 119.89 29.25 36637_at annexin A11 L19605 404.86118.94 29.38 40225_at cyclin G associated kinase D88435 385.87 114.6929.72 38744_at Deleted in split-hand/split-foot 1 region N95406 373.10109.49 29.35 32221_at PTD017 protein AL050361 371.70 108.89 29.301314_at proteasome (prosome| macropain) 26S subunit| non-ATPase| 1D44466 368.61 109.63 29.74 36208_at bromodomain-containing 2 D42040360.93 105.61 29.26 140_s_at splicing factor| arginine/serine-rich(transformer 2 Drosophila U68063 360.19 106.20 29.48 homolog) 1040979_at chromosome 14 open reading frame 3 AJ243310 355.27 106.33 29.9340610_at M-phase phosphoprotein homolog AI743507 344.58 101.36 29.4238703_at aspartyl aminopeptidase AF005050 339.21 100.19 29.54 38399_atsmall nuclear ribonucleoprotein polypeptide B″ AL034428 337.91 101.0529.90 38982_at TRF2-interacting telomeric RAP1 protein W28865 332.8096.76 29.07 1512_at dual-specificity tyrosine-(Y)-phosphorylationregulated kinase 1A D86550 330.61 97.02 29.35 38648_at trinucleotiderepeat containing 1 U80760 322.64 96.15 29.80 37731_at epidermal growthfactor receptor pathway substrate 15 Z29064 319.59 95.65 29.93 38472_atKIAA0143 protein D63477 318.06 94.20 29.62 38613_at putative cyclin G1interacting protein U61837 315.51 93.79 29.73 39686_g_at like mousebrain protein E46 AL050282 314.96 91.65 29.10 891_at YY1 transcriptionfactor M77698 313.42 93.44 29.81 38689_at hypothetical protein AL021937290.41 86.38 29.74 37517_at KIAA1039 protein AB028962 287.85 85.63 29.7534861_at golgi autoantigen| golgin subfamily a| 3 D63997 281.99 82.3829.21 39823_at H326 U06631 280.35 81.71 29.15 37581_at proteinphosphatase 6| catalytic subunit X92972 270.45 78.94 29.19 38977_attyrosyl-tRNA synthetase U89436 262.14 77.20 29.45 41763_g_at TIA1cytotoxic granule-associated RNA-binding protein-like 1 D64015 261.1178.14 29.93 37690_at ilvB (bacterial acetolactate synthase)-like U61263259.17 76.96 29.70 34323_at thyroid receptor interacting protein 15AF084260 259.01 75.79 29.26 33706_at squamous cell carcinoma antigenrecognised by T cells AB006198 255.89 74.35 29.06 40132_g_atfollistatin-like 1 D89937 253.42 74.99 29.59 34753_at synaptobrevin-like1 X92396 252.85 75.48 29.85 39601_at Ras association (RalGDS/AF-6)domain family 1 AF061836 251.76 74.05 29.41 34385_at succinatedehydrogenase complex| subunit C| integral membrane U57877 244.41 73.0929.91 protein| 15 kD 33301_g_at cell division cycle 2-like 1 (PITSLREproteins) AL031282 243.26 71.81 29.52 35301_at EST AL049941 236.41 69.6129.44 36535_at microfibrillar-associated protein 1 U04209 211.33 61.5529.13 34733_at splicing factor 3a| subunit 1| 120 kD X85237 210.62 61.1329.02 33268_at SMC (mouse) homolog| X chromosome L25270 201.57 59.5829.56 39746_at polymerase (RNA) ∥ (DNA directed) polypeptide B (140 kD)X63563 197.91 58.18 29.39 39380_at KIAA0697 protein AB014597 195.0458.16 29.82 40605_at sorting nexin 4 AA524345 189.00 55.74 29.49949_s_at proteasome (prosome| macropain) 26S subunit| ATPase| 6 D78275186.24 55.24 29.66 40623_at ubiquitin protein ligase AI749193 182.3453.45 29.31 37907_at coagulation factor VIII-associated (intronictranscript) M34677 181.01 53.35 29.47 229_at CCAAT-box-bindingtranscription factor M37197 112.31 33.26 29.61 37385_at Clk-associatingRS-cyclophilin U40763 86.32 25.20 29.19

TABLE 2 Fragment Mean % CV % CV No. Gene Name Ave. Diff. St_dev low PMThigh PMT 39415_at H. sapiens tunp mRNA for transformation upregulatednuclear 1026.88809 170.565203 17% 23% protein. 41194_at PT1.3_04_C04.rtumor1 Homo sapiens cDNA 5′, mRNA sequence. 1644.61573 279.769383 17%21% 33987_at Human ADP-ribosylation factor 1 (ARF1) mRNA, complete cds.1053.60427 184.57965 18% 24% 32575_at Human nucleosome assembly protein2 mRNA, complete cds. 477.012 84.240391 18% 22% 41785_at Human p97 mRNA,complete cds. 2146.16736 412.628482 19% 22% 39346_at Human p62 mRNA,complete cds. 546.721182 107.321822 20% 26% 31952_at H. sapiens mRNA forribosomal protein L6. 3206.74227 640.283429 20% 26% ns20e08.s1NCl_CGAP_GCB1 Homo sapiens cDNA clone 38084_at IMAGE:1184198 3′, mRNAsequence. 1118.78036 232.129292 21% 28% 35292_at H. sapiens BAT1 mRNAfor nuclear RNA helicase (DEAD family). 795.261727 167.254169 21% 26%39739_at Homo sapiens alpha NAC mRNA, complete cds. 2243.61464472.024126 21% 27% 33619_at Human ribosomal protein S13 (RPS13) mRNA,complete cds. 3007.25591 638.766828 21% 28% 38817_at Homo sapiens spermacrosomal protein mRNA, complete cds. 421.342818 90.0824915 21% 30%37321_at Human tetratricopeptide repeat protein (tpr1) mRNA, completecds. 354.162182 76.0661789 21% 26% 39027_at Homo sapiens cytochrome coxidase subunit IV precursor (COX4) 1335.39746 286.945221 21% 29% gene,nuclear gene encoding mitochondrial protein, complete cds. 40593_at H.sapiens mRNA for heterogeneous nuclear ribonucleoprotein. 1078.26327231.966596 22% 30% 35302_at Homo sapiens mRNA for TAP/NXF1 protein (nxf1gene). 334.106818 71.8899126 22% 26% 34608_at Human MHC proteinhomologous to chicken B complex protein 5005.15818 1077.96802 22% 29%mRNA, complete cds. 34570_at ubiquitin carboxyl extension protein[human, mRNA, 540 nt]. 2283.91418 493.661115 22% 28% 1653_at Human v-fostransformation effector protein (Fte-1), mRNA complete 3990.42273869.139812 22% 28% cds 33656_at Human mRNA for ribosomal protein L37,complete cds. 3596.03609 785.088807 22% 30% DKFZp761M078_s1 761(synonym: hamy2) Homo sapiens cDNA 33826_at clone DKFZp761M078 3′, mRNAsequence. 294.780091 64.3590978 22% 22% 36166_at Homo sapiens SPF31(SPF31) mRNA, complete cds. 226.214546 49.7114097 22% 25% 41224_at Homosapiens mRNA for KIAA0788 protein, partial cds. 564.298 125.081423 22%25% 35055_at H. sapiens BTF3b mRNA. 2535.722 562.331297 22% 24% 31708_atHomo sapiens ribosomal protein L30 mRNA, complete cds. 3124.15355692.861641 22% 27% 36972_at H. sapiens mRNA for transmembrane proteinrnp24. 866.941455 192.916911 22% 23% 32337_at Human ribosomal proteinL21 mRNA, complete cds. 2134.87055 475.979644 22% 27% 254_at Human H3.3histone class C mRNA, complete cds. 1413.40964 317.087392 22% 24%33660_at Human ribosomal protein L5 mRNA, complete cds. 2931.42864660.516812 23% 26% 32220_at Human mRNA for HMG-1, complete cds.746.693909 168.262743 23% 25% 34646_at H. sapiens gene for ribosomalprotein S7. 2500.63473 568.252652 23% 25% 40211_at Human gene forheterogeneous nuclear ribonucleoprotein (hnRNP) 1574.12555 360.03906523% 31% core protein A1. 37581_at H. sapiens mRNA for proteinphosphatase 6. 232.166273 53.1072301 23% 29% 38689_at Cluster InclAL021937: dJ149A16.6 (novel protein, human ortholog of 285.34890965.3091428 23% 30% worm F16A11.2 and bacterial and archea-bacterialpredicted proteins)/cds = (84,1601)/gb = AL021937/gi = 4165210/ug = Hs.10729/ len = 2014 38437_at H. sapiens MLN51 mRNA. 418.190273 95.771221123% 31% 505_at Human CDC37 homolog mRNA, complete cds. 670.117455154.995532 23% 22% 35125_at H. sapiens gene for ribosomal protein S6.3232.79191 747.844258 23% 28% 1315_at Human mRNA for ornithinedecarboxylase antizyme, ORF 1 and 4306.74709 998.152867 23% 29% ORF2.38672_at Homo sapiens fb19 mRNA. 158.562273 36.7548606 23% 22%qp51f08.x1 NCI_CGAP_Co8 Homo sapiens cDNA clone 37389_at IMAGE: 19265673′ similar to TR: O00193 O00193 SMALL ACIDIC 414.294546 96.1843904 23%25% PROTEIN.;, mRNA sequence. 34861_at Homo sapiens mRNA for GCP170,complete cds. 211.268818 49.1374269 23% 29% 35119_at H. sapiens mRNA for23 kD highly basic protein. 5442.70309 1279.01272 23% 29% 31385_at Humanribosomal protein L28 mRNA, complete cds. 6173.96791 1453.22923 24% 31%32437_at Human ribosomal protein S5 mRNA, complete cds. 4776.600911129.61556 24% 29% 1009_at Homo sapiens protein kinase C inhibitor(PKCI-1) mRNA, complete 1840.12073 435.694395 24% 27% cds. 33677_at Homosapiens ribosomal protein L30 mRNA, complete cds. 3565.723 844.72681224% 27% 40637_at Human hsc70 gene for 71 kd heat shock cognate protein.1347.46027 319.242248 24% 26% 32436_at Human ribosomal protein L27amRNA, complete cds. 3859.96082 916.763496 24% 29% 32436_at zk72a10.s1Soares_pregnant_uterus_NbHPU Homo sapiens cDNA 4142.93273 984.53904 24%27% clone IMAGE: 488346 3′ similar to gb: L19527 60S RIBOSOMAL PROTEINL27 (HUMAN);, mRNA sequence. 38061_at pec1.2-3.F11.r ecnorm Homo sapienscDNA 5′, mRNA sequence. 4709.65727 1120.18549 24% 30% 32553_at Humanzinc finger protein (MAZ) mRNA. 1324.87791 317.050776 24% 30% 32330_atHuman mRNA for ribosomal protein S11. 4781.80118 1145.31708 24% 29%38483_at Homo sapiens mRNA for hypothetical protein. 741.475091177.620755 24% 22% 33668_at Homo sapiens 60S ribosomal protein L12(RPL12) pseudogene, 3666.22155 879.972991 24% 30% partial sequence.36003_at Homo sapiens mRNA for poly(A)-specific ribonuclease. 152.45918236.7579511 24% 24% 39047_at Homo sapiens mRNA for squamous cellcarcinoma antigen SART-3, 250.677909 60.6222473 24% 24% complete cds.zu48g06.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 39811_atIMAGE: 741274 5′, mRNA sequence. 462.080364 111.804544 24% 21% 33614_atH. sapiens mRNA for ORF. 4438.22655 1076.78347 24% 29% 38046_at Homosapiens mRNA for Prer protein. 189.351636 45.9816717 24% 30% 36186_atHuman (clone E5.1) RNA-binding protein mRNA, complete cds. 1000.01436242.987057 24% 25% 38527_at Human 54 kDa protein mRNA, complete cds.1172.11364 285.380767 24% 27% 40426_at H. sapiens mRNA for BCL7Bprotein. 264.450818 64.4874354 24% 25% 40125_at Homo sapiens integralmembrane protein, calnexin, (IP90) mRNA, 1280.86518 312.743724 24% 24%complete cds. 37675_at H. sapiens mRNA for mitochondrial phosphatecarrier protein. 1634.062 399.04644 24% 28% 31546_at Homo sapiensribosomal protein L18 (RPL18) mRNA, complete cds. 3255.11446 796.14330424% 29% 40469_at Homo sapiens mRNA for KIAA0572 protein, partial cds.228.441546 56.0920217 25% 25% 34647_at Human mRNA for p68 protein.662.582455 162.814744 25% 30% 32315_at Human ribosomal protein S24 mRNA.3646.17255 899.123351 25% 27% 32241_at Homo sapiens mRNA; cDNADKFZp564O1716 (from clone 551.880091 136.161164 25% 25% DKFZp564O1716);complete cds. 32435_at H. sapiens mRNA for ribosomal protein L19.4612.49427 1138.57159 25% 28% 33659_at H. sapiens mRNA for non-muscletype cofilin. 4095.13346 1011.2557 25% 28% 37309_at Homo sapiens RHOAproto-oncogene multi-drug-resistance protein 2244.47327 554.267545 25%23% mRNA, 3′ end. 32039_at Homo sapiens beta-3A-adaptin subunit of theAP-3 complex mRNA, 202.007546 49.9878655 25% 26% complete cds. 31573_atHuman ribosomal protein S25 mRNA, complete cds. 3115.30918 775.8861 25%26% 38974_at Homo sapiens RNA-binding protein regulatory subunit mRNA,1349.68091 336.794841 25% 22% complete cds. 39727_at Homo sapiensprotein tyrosine phosphatase PIR1 mRNA, complete 187.273909 46.845235425% 31% cds. 36333_at H. sapiens mRNA for ribosomal protein L7.3379.63209 849.347293 25% 26% qa49c09.x1 Soares_NhHMPu_S1 Homo sapienscDNA clone 33861_at IMAGE: 1690096 3′, mRNA sequence. 152.20890938.2848254 25% 26% 32841_at Human nucleic acid binding protein gene,complete cds. 226.290818 56.9256749 25% 31% 41197_at Human mRNA forHHR23A protein, complete cds. 478.684091 120.69157 25% 29% 38654_at H.sapiens U21.1 mRNA. 229.842091 57.9601077 25% 30% 41833_at Homo sapienshJTB gene, complete cds. 1343.33582 338.936146 25% 22% 36786_at ClusterIncl AL022721: dJ109F14.2 (60S Ribosomal Protein RPL10A)/ 2589.09446654.928367 25% 31% cds = (15,668)/gb = AL022721/gi = 3367610/ug =Hs.76067/len = 703 39360_at Homo sapiens sorting nexin 3 (SNX3) mRNA,complete cds. 678.488727 171.970376 25% 22% 33984_at Human 90-kDaheat-shock protein gene, cDNA, complete cds. 2899.13164 734.823069 25%27% 32594_at Homo sapiens chaperonin containing t-complex polypeptide 1,delta 229.645182 58.2445319 25% 27% subunit (Cctd) mRNA, complete cds.1885_at Human DNA repair helicase (ERCC3) mRNA, complete cds. 154.33654639.2181176 25% 27% 39778_at Human N-acetylglucosaminyltransferase|(GlcNAc-TI) mRNA, 256.824727 65.2740889 25% 23% complete cds. 35298_atHomo sapiens translation initiation factor elF3 p66 subunit mRNA,1044.27864 265.763545 25% 28% complete cds. 41178_at H. sapiens mRNA forribosomal protein L11. 4617.69046 1176.58903 25% 28% 34864_at Homosapiens clone 24448 unknown mRNA, partial cds. 400.608273 102.132318 25%22% as86g01.x1 Barstead colon HPLRB7 Homo sapiens cDNA clone 34381_atIMAGE: 2335632 3′ similar to gb: X16560 CYTOCHROME C 1715.23391437.988735 26% 27% OXIDASE POLYPEPTIDE VIIC PRECURSOR (HUMAN);, mRNAsequence. 35835_at Homo sapiens mRNA, expressed in fibroblasts ofperiodontal 536.913 137.112927 26% 22% ligament, complete cds, clone:PDL-108. 36358_at Human ribosomal protein L9 mRNA, complete cds.3983.14173 1018.47768 26% 29% 31509_at H. sapiens BBC1 mRNA. 3235.68836828.95099 26% 27% 38542_at Homo sapiens nucleophosmin phosphoprotein(NPM) gene, 3′ 3789.96627 971.028442 26% 25% flankinq sequence. 38708_atHomo sapiens GTP binding protein mRNA, complete cds. 3069.247 787.55322826% 28% 38016_at Homo sapiens hnRNP-C like protein mRNA, complete cds.470.094 121.294239 26% 24% 34891_at PEC1.2_15_H01.r ecnorm Homo sapienscDNA 5′, mRNA 1695.08746 437.605159 26% 26% sequence. 41741_at Humanputative RNA binding protein RNPL mRNA, complete cds. 2346.64009605.819094 26% 29% 33666_at Human nuclear ribonucleoprotein particle(hnRNP) C protein mRNA, 857.862 221.645044 26% 25% complete cds.33667_at Human cyclophilin gene for cyclophilin (EC 5.2.1.8). 5131.125911326.01063 26% 28% 39141_at Homo sapiens TNF-alpha stimulated ABCprotein (ABC50) mRNA, 213.669727 55.328673 26% 28% complete cds.31583_at H. sapiens rpS8 gene for ribosomal protein S8. 4181.059821083.52675 26% 30% 32440_at Human L23 mRNA for putative ribosomalprotein. 3094.835 802.951872 26% 28% 36137_at H. sapiens mRNA for 218 kDMi-2 protein. 480.124818 124.737464 26% 25% DKFZp434A0418_s1 434(synonym: htes3) Homo sapiens cDNA 41295_at clone DKFZp434A0418 3′, mRNAsequence. 1030.45891 267.908852 26% 23% 39336_at Human ADP-ribosylationfactor 3 mRNA, complete cds. 670.617182 174.637432 26% 26% 632_at Homosapiens glycogen synthase kinase 3 mRNA, complete cds. 300.80254678.3361719 26% 24% 34592_at Human ribosomal protein S17 mRNA, completecds. 6148.256 1601.95246 26% 29% 39782_at H. sapiens mRNA for C1Dprotein. 444.403273 115.889308 26% 22% 37031_at Human mRNA for KIAA0183gene, partial cds. 213.145909 55.7684469 26% 27% 32644_at Homo sapiensmRNA for KIAA0169 protein, partial cds. 289.728273 75.8079662 26% 31%31907_at Homo sapiens mRNA for ribosomal protein L14, complete cds.2861.42573 748.942864 26% 26% 36676_at Cluster Incl AL031659:dJ343K2.2.1(ribophorin∥(isoform 1))/ 628.458 165.061493 26% 31% cds = (284,2179)/gb= AL031659/gi = 4468296/ug = Hs. 75722/ len = 2488 39050_at Homo sapienspoly(A) binding protein∥(PABP2) gene, complete 328.824273 86.4321681 26%30% cds. 39711_at Human 80K-H protein (kinase C substrate) mRNA,complete cds. 286.512455 75.4567186 26% 27% 891_at Homo sapiensGLI-Krupple related protein (YY1) mRNA, complete 194.662273 51.439218826% 30% cds. 41765_at pec1.2-4.D10.r ecnorm Homo sapiens cDNA 5′, mRNAsequence. 2895.27546 765.872869 26% 27% 40281_at Human mRNA for KIAA0158gene, complete cds. 1055.20136 279.345211 26% 26% wp10g06.x1NCI_CGAP_Kid12 Homo sapiens cDNA clone 35850_at IMAGE: 2464474 3′similar to WP: F29B9.4 CE09782;, mRNA 154.010818 40.7986435 26% 23%sequence. 35753_at Homo sapiens mRNA for PRP8 protein, complete cds.846.212273 224.661951 27% 22% 39079_at Homo sapiens mRNA for humanprotein homologous to DROER 949.239727 252.309065 27% 27% protein,complete cds. 33706_at Homo sapiens mRNA for SART-1, complete cds.264.590273 70.4664242 27% 29% 32438_at Homo sapiens ribosomal proteinS20 (RPS20) mRNA, complete cds. 5665.22391 1509.6601 27% 31% 36942_atHuman mRNA for KIAA0174 gene, complete cds. 302.519727 80.6550647 27%22% 1394_at Homo sapiens GTP-binding protein (rhoA) mRNA, complete cds.982.336 262.060927 27% 22% 1161_at Human 90 kD heat shock protein gene,complete cds. 3068.64864 818.752924 27% 29% 33657_at Homo sapiensribosomal protein L34 (RPL34) mRNA, complete cds. 3003.20536 801.90176627% 26% 36208_at Human mRNA for KIAA9001 gene, complete cds. 334.31272789.3038991 27% 29% wl57f04.x1 NCI_CGAP_Brn25 Homo sapiens cDNA clone39184_at IMAGE: 2429023 3′ similar to TR: Q15370 Q15370 RNA 781.212909209.195608 27% 24% POLYMERASE II TRANSCRIPTION FACTOR Sill P18 SUBUNIT;,mRNA sequence. 37717_at Human M4 protein mRNA, complete cds. 568.950182152.464818 27% 28% 1711_at Human clone 53BP1 p53-binding protein mRNA,partial cds. 132.636909 35.5821629 27% 26% 33913_at HumanHLA-B-associated transcript 2 (BAT2) mRNA, complete cds. 448.727182120.591553 27% 31% 39866_at Homo sapiens mRNA for KIAA1063 protein,partial cds. 872.284909 234.481854 27% 25% 777_at Human rab GDI mRNA,complete cds. 520.441909 140.415433 27% 30% 31538_at Human acidicribosomal phosphoprotein P0 mRNA, complete cds. 4749.375 1281.756 27%28% 36189_at Human nuclear factor NF45 mRNA, complete cds. 789.594091213.32811 27% 31% 38297_at H. sapiens mRNA for DRES9 protein. 329.37209188.9941743 27% 24% 38413_at Human mRNA for DAD-1, complete cds.520.306818 140.88454 27% 25% 39342_at H. sapiens mRNA for yeastmethionyl-tRNA synthetase homologue. 231.998182 62.8517235 27% 29%1499_at Human farnesyltransferase alpha-subunit mRNA, complete cds.439.475546 119.074695 27% 25% 32518_at Homo sapiens zinc finger protein(ZPR1) mRNA, complete cds. 236.681546 64.5653196 27% 30% 32573_atCluster Incl AL021546: Human DNA sequence from BAC 15E1 on 1153.58136315.372036 27% 28% chromosome 12. Contains Cytochrome C OxidasePolypeptide Vla- liver precursor gene, 605 ribosomal protein L31pseudogene, pre- mRNA splicing factor SRp30c gene, two putative genes,ESTs, STSs and putative CpG islands/cds = (52,717)/gb = AL021546/gi =2826890/ ug = Hs. 77608/len = 1069 31584_at Human mRNA fortranslationally controlled tumor protein. 2063.03309 564.60194 27% 28%33485_at Human mRNA for ribosomal protein, complete cds. 3501.35264958.722802 27% 27% 37040_at Human mRNA for KIAA0088 gene, partial cds.753.565182 207.00012 27% 24% 34336_at Homo sapiens mRNA for Lysyl tRNASynthetase, complete cds. 1035.29391 284.412474 27% 23% 38093_at Humanclone 23722 mRNA sequence. 195.475909 53.830052 28% 27% 33674_at H.sapiens mRNA for ribosomal protein L29. 4179.38646 1151.09042 28% 31%40824_at Homo sapiens mRNA for KIAA0745 protein, partial cds. 300.75172783.0648844 28% 23% 905_at Human guanylate kinase (GUK1) mRNA, completecds. 743.993 206.133175 28% 27% 31568_at Human ribosomal protein S10mRNA, complete cds. 5036.81646 1397.18081 28% 29% 36928_at H. sapiensOZF mRNA. 640.350636 177.964095 28% 27% 36035_at Homo sapiens mRNA forglycosylphosphatidylinositol anchor 423.229546 117.771247 28% 28%attachment 1 (GPAA1), complete cds. 35307_at Homo sapiens mRNA for GDPdissociation inhibitor beta. 1048.41582 291.769146 28% 23% 34231_at Homosapiens histone acetyltransferase (HBO1) mRNA, complete 156.49336443.5749228 28% 25% cds. 868_at Human TATA-binding protein associatedfactor 30 kDa subunit 616.615546 172.223284 28% 27% (taflI30) mRNA,complete cds. 32576_at Homo sapiens translation initiation factor 3 47kDa subunit mRNA, 1034.68636 289.205622 28% 28% complete cds. 38040_atHomo sapiens splicing factor mRNA, complete cds. 66.4970909 18.601135428% 30% 31955_at H. sapiens fau mRNA. 2940.44855 822.804695 28% 25%36587_at H. sapiens mRNA for elongation factor 2. 2335.08527 714.54496531% 25% 33875_at PN001_AH_H03.r yodnorm Homo sapiens cDNA 5′, mRNA565.580636 178.228414 32% 25% sequence. 1310_at Human mRNA forproteasome subunit HssC7-l, complete cds. 1616.867 522.128796 32% 28%41241_at Homo sapiens mRNA for Asparaginyl tRNA Synthetase, complete510.672455 174.096791 34% 25% cds. 36167_at Homo sapiens mRNA forproton-ATPase-like protein, complete cds. 713.034818 250.985814 35% 32%36138_at Human mRNA for calcium dependent protease (small subunit).1228.93318 451.389619 37% 27%

TABLE 3A Normal Tissue Summary Organ Morphology number of samplesADIPOSE TISSUE NORMAL TISSUE, NOS 11 AMYGDALOID NUCLEUS NORMAL TISSUE,NOS 1 BLADDER, NOS NORMAL TISSUE, NOS 1 BLOOD, NOS NORMAL TISSUE, NOS 6BLOOD, NOS 1 BONES, NOS DEGENERATION, NOS 3 BREAST, NOS NORMAL TISSUE,NOS 40 CEREBELLUM, NOS NORMAL TISSUE, NOS 1 CERVIX, NOS CHRONICINFLAMMATION, NOS 1 CERVIX, NOS MORPHOLOGY UNKNOWN 1 CERVIX, NOS NORMALTISSUE, NOS 35 COLON, NOS DILATATION, NOS 1 COLON, NOS NORMAL TISSUE,NOS 42 CORTEX OF FRONTAL LOBE NORMAL TISSUE, NOS 2 CORTEX OF PARIETALLOBE NORMAL TISSUE, NOS 1 CORTEX OF TEMPORAL LOBE NORMAL TISSUE, NOS 1DUODENUM, NOS NORMAL TISSUE, NOS 5 ENDOCERVIX SQUAMOUS METAPLASIA 1ENDOMETRIUM, NOS NORMAL TISSUE, NOS 8 ESOPHAGUS, NOS NORMAL TISSUE, NOS4 FALLOPIAN TUBE, NOS NORMAL TISSUE, NOS 3 FIBROUS TISSUE NORMAL TISSUE,NOS 1 GALLBLADDER, NOS CHRONIC INFLAMMATION, NOS 1 GALLBLADDER, NOSNORMAL TISSUE, NOS 1 KIDNEY, NOS NO PATHOLOGIC DIAGNOSIS 3 KIDNEY, NOSNORMAL TISSUE, NOS 13 LARYNX, NOS NORMAL TISSUE, NOS 2 LEFT ATRIUM, NOSNORMAL TISSUE, NOS 29 LIVER, NOS NORMAL TISSUE, NOS 7 LIVER, NOS 1 LUNG,NOS NORMAL TISSUE, NOS 25 LYMPH NODE, NOS NORMAL TISSUE, NOS 5 MUSCLES,NOS NORMAL TISSUE, NOS 7 MYOMETRIUM, NOS NORMAL TISSUE, NOS 39 OMENTUM,NOS NORMAL TISSUE, NOS 2 OVARY, NOS ATROPHY, NOS 1 OVARY, NOS NORMALTISSUE, NOS 18 PANCREAS, NOS NORMAL TISSUE, NOS 5 PARATHYROID GLAND, NOSNORMAL TISSUE, NOS 1 PLACENTA, NOS NORMAL TISSUE, NOS 1 PROSTATE, NOSNORMAL TISSUE, NOS 3 RECTUM, NOS NORMAL TISSUE, NOS 22 RIGHT ATRIUM, NOSNORMAL TISSUE, NOS 24 RIGHT VENTRICLE, NOS NORMAL TISSUE, NOS 30 SKIN,NOS NORMAL TISSUE, NOS 24 SMALL INTESTINE, NOS NORMAL TISSUE, NOS 16SPLEEN, NOS NORMAL TISSUE, NOS 10 STOMACH, NOS CHRONIC INFLAMMATION, NOS1 STOMACH, NOS NORMAL TISSUE, NOS 18 SUBSTANTIA NIGRA NORMAL TISSUE, NOS1 TESTIS, NOS NORMAL TISSUE, NOS 1 THYMUS, NOS NORMAL TISSUE, NOS 23THYROID GLAND, NOS CHRONIC INFLAMMATION, NOS 1 THYROID GLAND, NOS NORMALTISSUE, NOS 5 TONGUE, NOS NORMAL TISSUE, NOS 1 TONSIL, NOS LYMPHOIDHYPERPLASIA, NOS 10 URETER, NOS NORMAL TISSUE, NOS 1 UTERUS, NOSENDOMETRIOSIS, NOS 1 UTERUS, NOS NORMAL TISSUE, NOS 14 VEIN, NOS NORMALTISSUE, NOS 5 VULVA, NOS NORMAL TISSUE, NOS 2 WHITE BLOOD CELL, NOSNORMAL TISSUE, NOS 16 560

TABLE 3B Diseased Tissue Summary No. of Organ Morphology Samples ADRENALGLAND, NOS ADENOMA, NOS 1 ADRENAL GLAND, NOS ADRENAL CORTICAL CARCINOMA1 ADRENAL GLAND, NOS PHEOCHROMOCYTOMA, NOS 2 AMPULLA OF VATERADENOCARCINOMA, NOS 2 ARTERY, NOS ATHEROSCLEROSIS, NOS 1 BLADDER, NOSSPINDLE CELL CARCINOMA 1 BLADDER, NOS TRANSITIONAL CELL CARCINOMA, NOS 2BLOOD, NOS MORPHOLOGY NOT APPLICABLE 10 BONES, NOS DEGENERATION, NOS 9BONES, NOS GIANT CELL TUMOR OF BONE, NOS 1 BRAIN, NOS CHRONICINFLAMMATION, NOS 1 BRAIN, NOS MENINGIOMA, NOS 1 BREAST, NOSCYSTOSARCOMA PHYLLODES, NOS 2 BREAST, NOS FIBROADENOMA, NOS 2 BREAST,NOS FIBROCYSTIC DISEASE, NOS 3 BREAST, NOS HYPERTROPHY, NOS 1 BREAST,NOS INFILTRATING DUCT AND LOBULAR CARCINOMA 2 BREAST, NOS INFILTRATINGDUCT CARCINOMA 110 BREAST, NOS INFILTRATING LOBULAR CARCINOMA 10 BREAST,NOS INTRADUCTAL CARCINOMA, NOS 3 BREAST, NOS MEDULLARY CARCINOMA, NOS 2BREAST, NOS MUCINOUS ADENOCARCINOMA 1 BREAST, NOS NORMAL TISSUE, NOS 3BREAST, NOS PAPILLARY ADENOCARCINOMA, NOS 1 BREAST, NOS 7 CEREBELLUM,NOS ALZHEIMER'S NEUROFIBRILLARY DEGENERATION 1 CERVIX, NOSADENOCARCINOMA, NOS 2 CERVIX, NOS CARCINOMA, NOS 1 CERVIX, NOS CHRONICINFLAMMATION, NOS 3 CERVIX, NOS NEOPLASM, METASTATIC 1 CERVIX, NOSNORMAL TISSUE, NOS 1 CERVIX, NOS SQUAMOUS CELL CARCINOMA, NOS 3 COLON,NOS ACUTE AND CHRONIC INFLAMMATION, NOS 4 COLON, NOS ADENOCARCINOMA, NOS24 COLON, NOS ADENOMA, NOS 2 COLON, NOS CHRONIC INFLAMMATION, NOS 2COLON, NOS DIVERTICULITIS, NOS 1 COLON, NOS MUCINOUS ADENOCARCINOMA 5CORTEX OF FRONTAL LOBE ALZHEIMER'S NEUROFIBRILLARY DEGENERATION 3ENDOMETRIUM, NOS ADENOCARCINOMA, NOS 18 ENDOMETRIUM, NOS CHRONICINFLAMMATION, NOS 1 ENDOMETRIUM, NOS CLEAR CELL ADENOCARCINOMA, NOS 2ENDOMETRIUM, NOS HYPERPLASIA, NOS 1 ENDOMETRIUM, NOS MORPHOLOGY UNKNOWN1 ENDOMETRIUM, NOS MULLERIAN MIXED TUMOR 1 ENDOMETRIUM, NOS NEOPLASM,MALIGNANT 1 ENDOMETRIUM, NOS PAPILLARY SEROUS ADENOCARCINOMA 4ESOPHAGUS, NOS SQUAMOUS CELL CARCINOMA, NOS 1 ESOPHAGUS, NOS 2GALLBLADDER, NOS ACUTE AND CHRONIC INFLAMMATION, NOS 4 GALLBLADDER, NOSCHRONIC INFLAMMATION, NOS 16 KIDNEY, NOS ACUTE AND CHRONIC INFLAMMATION,NOS 1 KIDNEY, NOS CHRONIC INFLAMMATION, NOS 2 KIDNEY, NOS CLEAR CELLADENOCARCINOMA, NOS 11 KIDNEY, NOS CYST, NOS 1 KIDNEY, NOSGLOMERULOSCLEROSIS, NOS 5 KIDNEY, NOS MALIGNANT LYMPHOMA, NOS 1 KIDNEY,NOS ONCOCYTOMA 3 KIDNEY, NOS RENAL CELL CARCINOMA 10 KIDNEY, NOSTRANSITIONAL CELL CARCINOMA, NOS 1 KIDNEY, NOS WILMS' TUMOR 1 LACRIMALGLAND, NOS SQUAMOUS CELL CARCINOMA, NOS 1 LARYNX, NOS SQUAMOUS CELLCARCINOMA IN SITU, NOS 1 LARYNX, NOS SQUAMOUS CELL CARCINOMA, NOS 1 LEFTVENTRICLE, NOS NORMAL TISSUE, NOS 2 LEFT VENTRICLE, NOS 3 LIVER, NOSADENOCARCINOMA, NOS 1 LIVER, NOS ANGIOMYOSARCOMA 1 LIVER, NOS ATRESIA,NOS 1 LIVER, NOS CHRONIC INFLAMMATION, NOS 1 LIVER, NOS FIBROSIS, NOS 10LIVER, NOS FOCAL NODULAR HYPERPLASIA 2 LIVER, NOS HEPATOBLASTOMA 1LIVER, NOS HEPATOCELLULAR CARCINOMA, NOS 3 LIVER, NOS INFLAMMATION, NOS2 LUNG, NOS ADENOCARCINOMA, NOS 9 LUNG, NOS ADENOSQUAMOUS CARCINOMA 1LUNG, NOS CHRONIC INFLAMMATION, NOS 1 LUNG, NOS COLLAPSE, NOS 1 LUNG,NOS DILATATION, NOS 1 LUNG, NOS EMPHYSEMA, NOS 7 LUNG, NOS FIBROSIS, NOS1 LUNG, NOS NEOPLASM, MALIGNANT 1 LUNG, NOS NEOVASCULARIZATION 2 LUNG,NOS NEUROENDOCRINE CARCINOMA 1 LUNG, NOS NORMAL TISSUE, NOS 1 LUNG, NOSSPINDLE CELL SARCOMA 1 LUNG, NOS SQUAMOUS CELL CARCINOMA, NOS 6 LUNG,NOS 1 LYMPH NODE, NOS ADENOCARCINOMA, NOS 5 LYMPH NODE, NOS ATYPIASUSPICIOUS FOR MALIGNANCY 1 LYMPH NODE, NOS GRANULOMATOUS INFLAMMATION,NOS 1 LYMPH NODE, NOS HODGKIN'S DISEASE, NOS 3 LYMPH NODE, NOSINFILTRATING DUCT CARCINOMA 1 LYMPH NODE, NOS LYMPHOID HYPERPLASIA, NOS2 LYMPH NODE, NOS MALIGNANT LYMPHOMA, NOS 6 LYMPH NODE, NOS SIGNET RINGCELL CARCINOMA 1 LYMPH NODE, NOS SQUAMOUS CELL CARCINOMA, NOS 2MEDIASTINUM, NOS CARCINOMA, ANAPLASTIC, NOS 1 MEDIASTINUM, NOSNEUROBLASTOMA, NOS 1 MEDIASTINUM, NOS SCHWANNOMA, NOS 1 MEDULLA OFKIDNEY CHRONIC INFLAMMATION, NOS 1 MESENTERY, NOS ADENOCARCINOMA, NOS 1MUSCLES, NOS ATROPHY, NOS 2 MYOMETRIUM, NOS ADENOCARCINOMA, METASTATIC,NOS 1 MYOMETRIUM, NOS ATROPHY, NOS 1 MYOMETRIUM, NOS ENDOMETRIOSIS, NOS2 MYOMETRIUM, NOS LEIOMYOMA, NOS 26 NASOPHARYNX, NOS SQUAMOUS CELLCARCINOMA, NOS 1 OMENTUM, NOS ADENOCARCINOMA, NOS 2 OMENTUM, NOSPAPILLARY SEROUS ADENOCARCINOMA 9 OMENTUM, NOS SIGNET RING CELLCARCINOMA 1 OVARY, NOS ABSCESS 1 OVARY, NOS ADENOCARCINOMA, NOS 7 OVARY,NOS CARCINOID TUMOR, NOS (EXCEPT OF APPENDIX, M-82401) 1 OVARY, NOSCARCINOMA, NOS 1 OVARY, NOS CLEAR CELL ADENOCARCINOMA, NOS 1 OVARY, NOSDYSGERMINOMA 1 OVARY, NOS ENDOMETRIOID CYSTADENOFIBROMA, BORDERLINEMALIGNANCY 1 OVARY, NOS GRANULOSA CELL TUMOR, NOS 1 OVARY, NOS MUCINOUSCYSTADENOCARCINOMA, NOS 2 OVARY, NOS MULLERIAN MIXED TUMOR 2 OVARY, NOSPAPILLARY SEROUS ADENOCARCINOMA 8 OVARY, NOS PAPILLARY SEROUS TUMOR OFLOW MALIGNANT POTENTIAL 1 OVARY, NOS POLYCYSTIC CHANGE, NOS 1 OVARY, NOSSEROUS CYSTADENOCARCINOMA, NOS 3 OVARY, NOS SEROUS CYSTADENOFIBROMA 1OVARY, NOS STRUMA OVARII, NOS 2 OVARY, NOS THECOMA, NOS 2 PANCREAS, NOSADENOCARCINOMA, NOS 10 PANCREAS, NOS CHRONIC INFLAMMATION, NOS 2PANCREAS, NOS MICROCYSTIC ADENOMA 1 PANCREAS, NOS SCLEROSINGINFLAMMATION, NOS 1 PARATHYROID GLAND, NOS ADENOMA, NOS 1 PAROTID GLAND,NOS CARCINOMA IN PLEOMORPHIC ADENOMA 1 PAROTID GLAND, NOS WARTHIN'STUMOR 1 PERITONEUM, NOS PAPILLARY SEROUS ADENOCARCINOMA 1 PERITONEUM,NOS SARCOMA, NOS 1 PROSTATE, NOS ADENOCARCINOMA, NOS 5 PROSTATE, NOSNODULAR HYPERPLASIA 12 RECTUM, NOS ADENOCARCINOMA IN SITU, NOS 1 RECTUM,NOS ADENOCARCINOMA, NOS 20 RECTUM, NOS ADENOMA, NOS 1 RECTUM, NOSCHRONIC INFLAMMATION, NOS 3 RECTUM, NOS MUCINOUS ADENOCARCINOMA 1SALIVARY GLAND, NOS ADENOID CYSTIC CARCINOMA 1 SKIN, NOS ADNEXAL TUMOR 1SKIN, NOS BASAL CELL CARCINOMA, NOS 4 SKIN, NOS HEMANGIOMA, NOS 1 SKIN,NOS MALIGNANT MELANOMA, NOS 1 SKIN, NOS MELANOCYTIC HYPERPLASIA 1 SKIN,NOS SQUAMOUS CELL CARCINOMA, NOS 4 SMALL INTESTINE, NOS ADENOCARCINOMA,NOS 1 SMALL INTESTINE, NOS MALIGNANT LYMPHOMA, NOS 2 SOFT TISSUES, NOSANGIOSARCOMA 2 SOFT TISSUES, NOS CARCINOMA IN PLEOMORPHIC ADENOMA 1 SOFTTISSUES, NOS FIBROMA, NOS 1 SOFT TISSUES, NOS FIBROMATOSIS, NOS 1 SOFTTISSUES, NOS FIBROUS HISTIOCYTOMA, MALIGNANT 4 SOFT TISSUES, NOSHEMANGIOMA, NOS 1 SOFT TISSUES, NOS LEIOMYOSARCOMA, NOS 2 SOFT TISSUES,NOS LIPOMA, NOS 3 SOFT TISSUES, NOS LIPOMATOSIS, NOS 1 SOFT TISSUES, NOSLIPOSARCOMA, NOS 2 SOFT TISSUES, NOS SQUAMOUS CELL CARCINOMA, NOS 1 SOFTTISSUES, NOS SYNOVIAL SARCOMA, NOS 1 SPLEEN, NOS ABERRANT TISSUE, NOS 2SPLEEN, NOS CHRONIC MYELOID LEUKEMIA 3 SPLEEN, NOS GRANULOMATOUSINFLAMMATION, NOS 1 SPLEEN, NOS HYPERTROPHY, NOS 1 SPLEEN, NOS MALIGNANTLYMPHOMA, NOS 2 STOMACH, NOS ADENOCARCINOID TUMOR 1 STOMACH, NOSADENOCARCINOMA, NOS 21 STOMACH, NOS ATYPIA SUSPICIOUS FOR MALIGNANCY 1STOMACH, NOS CARCINOMA, NOS 1 STOMACH, NOS CHRONIC INFLAMMATION, NOS 8STOMACH, NOS HYPERTROPHY, NOS 1 STOMACH, NOS SIGNET RING CELL CARCINOMA2 STOMACH, NOS 1 SYNOVIUM OF JOINT, NOS PROLIFERATION, NOS 1 TESTIS, NOSMIXED GERM CELL TUMOR 1 TESTIS, NOS SEMINOMA, NOS 2 THYMUS, NOS ATROPHY,NOS 1 THYMUS, NOS LYMPHOID HYPERPLASIA, NOS 1 THYROID GLAND, NOSCARCINOMA, ANAPLASTIC, NOS 1 THYROID GLAND, NOS CHRONIC INFLAMMATION,NOS 5 THYROID GLAND, NOS FOLLICULAR ADENOCARCINOMA, NOS 1 THYROID GLAND,NOS MALIGNANT LYMPHOMA, NOS 1 THYROID GLAND, NOS NODULAR HYPERPLASIA 16THYROID GLAND, NOS PAPILLARY CARCINOMA, NOS 4 TONGUE, NOS SQUAMOUS CELLCARCINOMA, NOS 3 TONSIL, NOS LYMPHOID HYPERPLASIA, NOS 10 UTERUS, NOSADENOCARCINOMA, NOS 1 VULVA, NOS SQUAMOUS CELL CARCINOMA, NOS 5 WHITEBLOOD CELL, NOS 7 695

TABLE 4 AFFX fragment Forward Primer Reverse Primer TaqMan probe ID GeneName (Name/sequence) (Name/sequence (Name/sequence 39360_at sortingnexin 3 AF034546-83F/ af034546-201R/ af034546-112T/ AAGCCGCAGAACACCCTGATTTC ACCCCCCAGCAA CTGAATGA GTAAGTGGTGA CTTCCTCGAGAT A C 36027_atpolymerase AA418779- aa418779- aa418779-382T (RNA) II (DNA 362Forward/33Reverse/ Sequence/ATCCCC directed) AGGAACTCAAGG CCCAGTCTTCAATCATCATTCGC polypeptide F CCCGAAA TAGCTCCCATC CGTTACC T 34849_atseryl-tRNA x91257- x91257- x91257-1278T/ synthetase 1254Forward/1342Reverse/ CCAGGCTCGCCG CTCCTGTTCTAA CAAACTCCACC GCTTCGA TTGCACGGATTTTGTCCATCAT C

1. A method of identifying at least one gene that is consistentlyexpressed across different cell or tissue types in an organism,comprising: (a) preparing gene expression profiles for different cell ortissue types from the organism; (b) calculating a coefficient ofvariation for at least one gene in each of the profiles across thedifferent cell or tissue types; and (c) selecting any gene whosecoefficient of variation indicates that the gene is consistentlyexpressed across the different cell or tissue types.
 2. A method ofclaim 1, wherein step (c) comprises identifying at least one gene with acoefficient of variation of less than about 40%.
 3. A method of claim 1,wherein the different cell or tissue types comprise greater than about10 different cell or tissue types.
 4. A method of claim 1, wherein thedifferent cell or tissue types comprise greater than about 25 differentcell or tissue types.
 5. A method of claim 1, wherein the different cellor tissue types comprise greater than about 50 different cell or tissuetypes.
 6. A method of claim 3, wherein the cell or tissue types comprisenormal and diseased cell or tissue types.
 7. A method of claim 1,wherein the organism is a mammal or plant.
 8. A method of claim 7,wherein the mammal is human, dog, rat, mouse or plant.
 9. A method ofclaim 8, wherein the expression profiles are generated by querying agene expression database for the expression level of at least one genein different cell or tissue types from the organism or from a cell line.10. A set of probes comprising at least two probes that specificallyhybridize to a gene identified by the method of claim
 1. 11. A set ofprobes according to claim 10, wherein the set comprises probes thatspecifically hybridize to at least about 10 genes.
 12. A set of probesaccording to claim 10, wherein the set comprises probes thatspecifically hybridize to at least about 25 genes.
 13. A set of probesaccording to claim 10, wherein the set comprises probes thatspecifically hybridize to at least about 50 genes.
 14. A set of probesaccording to claim 10, wherein the set comprises probes thatspecifically hybridize to at least about 100 genes.
 15. A set of probesaccording to claim 10, wherein the probes are attached to a single solidsubstrate.
 16. A set of probes of claim 15, wherein the solid substrateis a chip.
 17. A method of normalizing the data from a nucleic aciddetection assay comprising: (a) detecting the expression level for atleast one gene in a nucleic acid sample; and (b) normalizing theexpression of said at least one gene with the detected expression of ancontrol gene identified by the method of claim
 1. 18. A method of claim17, wherein step (b) comprises normalizing the expression level of saidat least one gene with the expression levels of at least about 10control genes.
 19. A method of claim 17, wherein step (b) comprisesnormalizing the expression level of said at least one gene with theexpression levels of at least about 25 control genes.
 20. A method ofclaim 17, wherein step (b) comprises normalizing the expression level ofsaid at least one gene with the expression levels of at least about 50control genes.
 21. A method of claim 17, wherein step (b) comprisesnormalizing the expression level of said at least one gene with theexpression levels of at least about 100 control genes.
 22. A method ofclaim 17, wherein the assay is quantitative.
 23. A method of claim 17,wherein the assay is a hybridization reaction conducted on a solidsubstrate.
 24. A method of claim 23, wherein the solid substrate is anoligonucleotide array.
 25. A method of claim 24, wherein the arraycomprises oligonucleotide probes that are complementary to the controlgenes.
 26. A method of claim 17, wherein the assay is a polymerase chainreaction.
 27. A set of probes comprising at least two probes thatspecifically hybridize to a gene of Table 1 or Table
 2. 28. A set ofprobes of claim 27, comprising probes that specifically hybridize to atleast about 10 genes of Table 1 or Table
 2. 29. A set of probes of claim27, comprising probes that specifically hybridize to at least about 25genes of Table 1 or Table
 2. 30. A set of probes of claim 27, comprisingprobes that specifically hybridize to at least about 50 genes of Table 1or Table
 2. 31. A set of probes of claim 27, comprising probes thatspecifically hybridize to at least about 100 genes of Table 1 or Table2.
 32. A set of probes of claim 27, comprising probes that specificallyhybridize to at least about 100 genes of Table
 2. 33. A set of probes ofclaim 27, wherein the probes are attached to a single solid substrate.34. A set of probes of claim 33, wherein the solid substrate is a chip.35. A method of normalizing the data from a nucleic acid detection assaycomprising: (a) detecting the expression level for at least one gene ina nucleic acid sample; and (b) normalizing the expression of said atleast one gene with the detected expression of a control gene of Table 1or Table
 2. 36. A method of claim 35, wherein step (b) comprisesnormalizing the expression level of said at least one gene with theexpression levels of at least about 10 control genes of Table 1 or Table2.
 37. A method of claim 35, wherein step (b) comprises normalizing theexpression level of said at least one gene with the expression levels ofat least about 25 control genes of Table 1 or Table
 2. 38. A method ofclaim 35, wherein step (b) comprises normalizing the expression level ofsaid at least one gene with the expression levels of at least about 50control genes of Table 1 or Table
 2. 39. A method of claim 35, whereinstep (b) comprises normalizing the expression level of said at least onegene with the expression levels of at least about 100 control genes ofTable 1 or Table
 2. 40. A method of claim 35, wherein the assay isquantitative.
 41. A method of claim 35, wherein the assay is ahybridization reaction conducted on a solid substrate.
 42. A method ofclaim 41, wherein the solid substrate is an oligonucleotide array.
 43. Amethod of claim 42, wherein the array comprises oligonucleotide probesthat are complementary to the control genes.
 44. A method of claim 35,wherein the assay is a polymerase chain reaction.
 45. A method of claim17, wherein the normalizing of step (b) comprises dividing theexpression level for said at least one gene by the detected expressionlevel of said control gene.
 46. A method of identifying at least onegene that is consistently expressed across different cell or tissuetypes in an organism or cell line, comprising: (a) querying a geneexpression database for the expression level of at least one gene indifferent cell or tissue types from the organism or cell lines; (b)calculating a coefficient of variation for said at least one gene acrossthe different cell or tissue types or cell lines; and (c) identifying atleast one gene whose coefficient of variation indicates that the gene isconsistently expressed across the different cell or tissue types or celllines.
 47. A method of claim 46, wherein step (c) comprises identifyingat least one gene with a coefficient of variation of less than about40%.
 48. A method of claim 47, wherein the different cell or tissuetypes comprise greater than about 10 different cell or tissue types. 49.A method of claim 47, wherein the different cell or tissue typescomprise greater than about 25 different cell or tissue types.
 50. Amethod of claim 47, wherein the different cell or tissue types comprisegreater than about 50 different cell or tissue types.
 51. A method ofclaim 46, wherein the cell or tissue types comprise normal and diseasedcell or tissue types.
 52. A method of claim 47, wherein the organism isa mammal or plant.
 53. A method of claim 52, wherein the mammal ishuman, rat, mouse or plant.
 54. A method of claim 53, wherein the mammalis human.